https://wiki.anunna.wur.nl/api.php?action=feedcontributions&feedformat=atom&user=Derks047
HPCwiki - User contributions [en]
2026-06-19T07:14:52Z
User contributions
MediaWiki 1.45.3
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=2060
JBrowse
2019-11-25T09:33:55Z
<p>Derks047: /* Add annotation files (GFF/BED) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/Cyprinus_carpio/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Make a directory in <code>/cm/shared/apps/jbrowse/</code> for your species of interested (e.g. <code>mkdir Cyprinus_carpio</code>). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
mv JBrowse-1.12.0/* $PWD<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Genes" --type gene --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`echo $bam | rev | cut -c 5- | cut -d'/' -f1 | rev` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
You can load single BigWig-files by following command:<br />
<source lang='bash'><br />
bin/add-bw-track --label <label> --bw_url <url><br />
</source><br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl<br />
</source><br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1756
JBrowse
2017-03-07T15:19:57Z
<p>Derks047: /* Wiggle/BigWig tracks (WIG) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/Cyprinus_carpio/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Make a directory in <code>/cm/shared/apps/jbrowse/</code> for your species of interested (e.g. <code>mkdir Cyprinus_carpio</code>). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
mv JBrowse-1.12.0/* $PWD<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`echo $bam | rev | cut -c 5- | cut -d'/' -f1 | rev` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
You can load single BigWig-files by following command:<br />
<source lang='bash'><br />
bin/add-bw-track --label <label> --bw_url <url><br />
</source><br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl<br />
</source><br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1755
JBrowse
2017-03-07T15:19:03Z
<p>Derks047: /* Wiggle/BigWig tracks (WIG) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/Cyprinus_carpio/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Make a directory in <code>/cm/shared/apps/jbrowse/</code> for your species of interested (e.g. <code>mkdir Cyprinus_carpio</code>). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
mv JBrowse-1.12.0/* $PWD<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`echo $bam | rev | cut -c 5- | cut -d'/' -f1 | rev` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
You can load single BigWig-files by following command:<br />
<source lang='bash'><br />
bin/add-bw-track --label <label> --bam_url <url><br />
</source><br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl<br />
</source><br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1741
JBrowse
2016-02-23T15:28:05Z
<p>Derks047: </p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`echo $bam | rev | cut -c 5- | cut -d'/' -f1 | rev` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
You can load single BigWig-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bw in /lustre/nobackup/WUR/ABGC/shared/Chicken/Ensembl_Rna_Seq/*.bw; do<br />
ln -s $bw track_symlinks/<br />
tissue=`echo $bw | rev | cut -c 8- | cut -d'/' -f1 | rev`<br />
echo '{<br />
"label" : "'${tissue}'_BWcoverage",<br />
"key" : "'${tissue}'_BWcoverage",<br />
"storeClass" : "BigWig",<br />
"urlTemplate" : "../track_symlinks/'${tissue}.bam.bw'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "JBrowse/View/Track/Wiggle/XYPlot",<br />
"variance_band" : true<br />
}' | bin/add-track-json.pl data/trackList.json<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl<br />
</source><br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1740
JBrowse
2016-02-23T15:17:56Z
<p>Derks047: /* Alignment tracks (BAM) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`echo $bam | rev | cut -c 5- | rev | cut -d'/' -f9` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
You can load single BigWig-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bw in /lustre/nobackup/WUR/ABGC/shared/Chicken/Ensembl_Rna_Seq/*.bw; do<br />
ln -s $bw track_symlinks/<br />
tissue=`echo $bw | rev | cut -c 8- | rev | cut -d'/' -f9`<br />
echo '{<br />
"label" : "'${tissue}'_BWcoverage",<br />
"key" : "'${tissue}'_BWcoverage",<br />
"storeClass" : "BigWig",<br />
"urlTemplate" : "../track_symlinks/'${tissue}.bam.bw'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "JBrowse/View/Track/Wiggle/XYPlot",<br />
"variance_band" : true<br />
}' | bin/add-track-json.pl data/trackList.json<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl<br />
</source><br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1739
JBrowse
2016-02-23T15:12:36Z
<p>Derks047: /* Wiggle/BigWig tracks (WIG) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
You can load single BigWig-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bw in /lustre/nobackup/WUR/ABGC/shared/Chicken/Ensembl_Rna_Seq/*.bw; do<br />
ln -s $bw track_symlinks/<br />
tissue=`echo $bw | rev | cut -c 8- | rev | cut -d'/' -f9`<br />
echo '{<br />
"label" : "'${tissue}'_BWcoverage",<br />
"key" : "'${tissue}'_BWcoverage",<br />
"storeClass" : "BigWig",<br />
"urlTemplate" : "../track_symlinks/'${tissue}.bam.bw'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "JBrowse/View/Track/Wiggle/XYPlot",<br />
"variance_band" : true<br />
}' | bin/add-track-json.pl data/trackList.json<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl<br />
</source><br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1738
JBrowse
2016-02-23T15:11:35Z
<p>Derks047: /* Wiggle/BigWig tracks (WIG) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
You can load single BigWig-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/<br />
ln -s $bam.bai track_symlinks/<br />
tissue=`echo $bam | rev | cut -c 5- | rev | cut -d'/' -f9`<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}.bam'",<br />
"category" : "3. ENSEMBL RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${tissue}.bam'",<br />
"category" : "3. ENSEMBL RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl<br />
</source><br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1737
JBrowse
2016-02-23T13:50:45Z
<p>Derks047: /* Evidence tracks */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl<br />
</source><br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1736
JBrowse
2016-02-23T13:50:19Z
<p>Derks047: /* Evidence tracks */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using <br />
<br />
bin/flatfile-to-json.pl<br />
<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1735
JBrowse
2016-02-23T13:50:05Z
<p>Derks047: /* Evidence tracks */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===<br />
<br />
Evidence tracks can be loaded in bed, gff and gbk format using bin/flatfile-to-json.pl<br />
Examples are given above.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1734
JBrowse
2016-02-23T13:49:13Z
<p>Derks047: /* Variant tracks (VCF) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<source lang='bash'><br />
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
</source><br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1733
JBrowse
2016-02-23T13:48:33Z
<p>Derks047: /* Variant tracks (VCF) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
To load a VCF file in JBrowse make sure the file is gzipped and indexed<br />
<br />
<br />
echo ' {<br />
"label" : "Gallus_gallus_incl_consequences",<br />
"key" : "Gallus_gallus_incl_consequences",<br />
"storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",<br />
"urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",<br />
"category" : "2. Variants",<br />
"type" : "HTMLVariants"<br />
} ' | bin/add-track-json.pl data/trackList.json<br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1732
JBrowse
2016-02-23T13:45:32Z
<p>Derks047: /* Alignment tracks (BAM) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
</source><br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source><br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1731
JBrowse
2016-02-23T13:45:04Z
<p>Derks047: /* Alignment tracks (BAM) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files<br />
tissue=`${bam::-4}` ## USe the name of the file without .bam as trackLabel<br />
<br />
## Add BAM in alignment mode (Alignments2)<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
## Add BAM in coverage mode (SNPCoverage)<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source<br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1730
JBrowse
2016-02-23T13:43:08Z
<p>Derks047: /* Alignment tracks (BAM) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
To load multiple BAM files present in a certain directory use:<br />
<source lang='bash'><br />
<br />
for bam in /<dir>*.bam; do<br />
ln -s $bam track_symlinks/ ## Make symlinks from the BAM files<br />
ln -s $bam.bai track_symlinks/<br />
tissue=`${bam::-4}`<br />
echo $tissue<br />
echo '{<br />
"label" : "'${tissue}'_alignment",<br />
"key" : "'${tissue}'_alignment",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "Alignments2"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
echo '{<br />
"label" : "'${tissue}'_coverage",<br />
"key" : "'${tissue}'_coverage",<br />
"storeClass" : "JBrowse/Store/SeqFeature/BAM",<br />
"urlTemplate" : "../track_symlinks/'${bam}'",<br />
"category" : "3. RNA-seq alignments",<br />
"type" : "SNPCoverage"<br />
}' | bin/add-track-json.pl data/trackList.json<br />
<br />
done<br />
<br />
Make sure the BAM file can be read by a everybody if not use:<br />
<source lang='bash'><br />
chmod +r <BAM_file><br />
</source<br />
<br />
Make sure that all directoryies in the full path of the BAMfile are executable:<br />
<source lang='bash'><br />
chmod +x <dir><br />
</source<br />
<br />
<br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1729
JBrowse
2016-02-23T13:39:35Z
<p>Derks047: /* Alignment tracks (BAM) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
You can load single BAM-files by following command:<br />
<source lang='bash'><br />
bin/add-bam-track --label <label> --bam_url <url><br />
</source><br />
<br />
===Variant tracks (VCF)===<br />
<br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1727
JBrowse
2016-01-28T15:29:44Z
<p>Derks047: </p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
===Alignment tracks (BAM)===<br />
<br />
<br />
===Variant tracks (VCF)===<br />
<br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1726
JBrowse
2016-01-28T15:29:33Z
<p>Derks047: </p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
<br />
===Alignment tracks (BAM)===<br />
<br />
<br />
===Variant tracks (VCF)===<br />
<br />
<br />
===Wiggle/BigWig tracks (WIG)===<br />
<br />
<br />
===Evidence tracks===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1725
JBrowse
2016-01-28T15:29:03Z
<p>Derks047: </p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
<br />
===Alignment tracks (BAM) ===<br />
<br />
<br />
===Variant tracks (VCF) ===<br />
<br />
<br />
===Wiggle/BigWig tracks (VCF) ===<br />
<br />
<br />
===Evidence tracks ===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1724
JBrowse
2016-01-28T14:42:36Z
<p>Derks047: /* Add annotation files (GFF/BED) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source><br />
<br />
Add corresponding transcripts:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3<br />
</source></div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1723
JBrowse
2016-01-28T14:41:04Z
<p>Derks047: /* Add annotation files (GFF/BED) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
<source lang='bash'><br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/gg_test.gff3<br />
</source></div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1722
JBrowse
2016-01-28T14:40:47Z
<p>Derks047: /* Add annotation files (GFF/BED) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html<br />
<br />
Add gene features:<br />
<br />
bin/flatfile-to-json.pl --key "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/gg_test.gff3</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1721
JBrowse
2016-01-28T14:26:20Z
<p>Derks047: /* Add reference sequence */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
To remove tracks use following command:<br />
<br />
<source lang='bash'><br />
bin/remove-track.pl -D --trackLabel 'trackname'<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1720
JBrowse
2016-01-28T13:58:54Z
<p>Derks047: /* Add annotation files (GFF/BED) */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===<br />
<br />
Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1719
JBrowse
2016-01-27T14:36:10Z
<p>Derks047: /* Trim sequences for quality and adapters */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
===Add annotation files (GFF/BED)===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1718
JBrowse
2016-01-27T14:35:47Z
<p>Derks047: /* Add reference sequence */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
Example code for chicken genome<br />
<br />
<source lang='bash'><br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
</source><br />
<br />
===Trim sequences for quality and adapters===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1717
JBrowse
2016-01-27T14:35:08Z
<p>Derks047: /* Add reference sequence */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa<br />
<br />
===Trim sequences for quality and adapters===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1716
JBrowse
2016-01-27T08:55:14Z
<p>Derks047: /* Typical commands used to set up a JBrowse */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
<br />
=== Install JBrowse ===<br />
<br />
Download the latest JBrowse here: http://jbrowse.org/<br />
<br />
Run the setup script to install perl dependencies and required modules<br />
<br />
<source lang='bash'><br />
unzip JBrowse-1.12.0.zip<br />
./setup.sh<br />
</source><br />
<br />
=== Add reference sequence ===<br />
<br />
===Trim sequences for quality and adapters===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1715
JBrowse
2016-01-27T08:50:52Z
<p>Derks047: /* Typical commands used to set up a JBrowse */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
* Users are free to add usefull commands to this tutorial<br />
* Use case in wintermoth. 12 samples (1 Egg, 1 Caterpillar, 3x3 Pupa, 1 Moth).<br />
<br />
===Trim sequences for quality and adapters===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1714
JBrowse
2016-01-27T08:50:36Z
<p>Derks047: /* Typical commands used to set up a JBrowse */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
** https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
<br />
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
<br />
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
<br />
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
<br />
* Users are free to add usefull commands to this tutorial<br />
* Use case in wintermoth. 12 samples (1 Egg, 1 Caterpillar, 3x3 Pupa, 1 Moth).<br />
<br />
===Trim sequences for quality and adapters===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1713
JBrowse
2016-01-27T08:48:30Z
<p>Derks047: /* Typical commands used to set up a JBrowse */</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
- https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
<br />
- https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
<br />
- https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
<br />
- https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
<br />
* Users are free to add usefull commands to this tutorial<br />
* Use case in wintermoth. 12 samples (1 Egg, 1 Caterpillar, 3x3 Pupa, 1 Moth).<br />
<br />
===Trim sequences for quality and adapters===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=JBrowse&diff=1712
JBrowse
2016-01-27T08:48:18Z
<p>Derks047: Created page with "=== Typical commands used to set up a JBrowse === Author: Martijn Derks * JBrowse is available for multiple species: - https://jbrowse.hpcagrogenomics.wur.nl/pig/ - https:/..."</p>
<hr />
<div>=== Typical commands used to set up a JBrowse === <br />
<br />
Author: Martijn Derks<br />
<br />
* JBrowse is available for multiple species:<br />
- https://jbrowse.hpcagrogenomics.wur.nl/pig/<br />
- https://jbrowse.hpcagrogenomics.wur.nl/chicken/<br />
- https://jbrowse.hpcagrogenomics.wur.nl/cattle/<br />
- https://jbrowse.hpcagrogenomics.wur.nl/turkey/<br />
<br />
* Users are free to add usefull commands to this tutorial<br />
* Use case in wintermoth. 12 samples (1 Egg, 1 Caterpillar, 3x3 Pupa, 1 Moth).<br />
<br />
===Trim sequences for quality and adapters===</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=User:Derks047&diff=1639
User:Derks047
2016-01-20T13:48:33Z
<p>Derks047: </p>
<hr />
<div>I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations. I'm experienced in Genomics (de novo genome assembly & annotation), Transcriptomics (mapping, quantification and differential expression) and Epigenomics (whole genome methylation).<br />
<br><br />
Google scholar: [https://scholar.google.nl/citations?user=aoAn0eAAAAAJ&hl=nl&oi=sra Google scholar ]<br />
<br><br />
WUR profile: [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=49317 WUR-profile]</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=User:Derks047&diff=1638
User:Derks047
2016-01-20T13:46:51Z
<p>Derks047: </p>
<hr />
<div>I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations. I'am also very experienced in de novo genome assembly & annotation.<br />
<br><br />
Google scholar: [https://scholar.google.nl/citations?user=aoAn0eAAAAAJ&hl=nl&oi=sra Google scholar ]<br />
<br><br />
WUR profile: [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=49317 WUR-profile]</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=User:Derks047&diff=1637
User:Derks047
2016-01-20T13:46:23Z
<p>Derks047: </p>
<hr />
<div>I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations. I'am also very experienced in de novo genome assembly & annotation.<br />
Google scholar: [https://scholar.google.nl/citations?user=aoAn0eAAAAAJ&hl=nl&oi=sra | Google scholar ]<br />
WUR profile: [https://www.vcard.wur.nl/Views/Profile/View.aspx?id=49317 | WUR-profile]</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=User:Derks047&diff=1636
User:Derks047
2016-01-20T13:45:03Z
<p>Derks047: </p>
<hr />
<div>I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations. I'am also very experienced in de novo genome assembly & annotation.<br />
For more information find my google scholar and wur profile page: [[https://scholar.google.nl/citations?user=aoAn0eAAAAAJ&hl=nl&oi=sra | Google scholar ]]</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=User:Derks047&diff=1635
User:Derks047
2016-01-20T13:43:06Z
<p>Derks047: </p>
<hr />
<div>I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations. I'am also very experienced in de novo genome assembly & annotation.<br />
For more information: https://scholar.google.nl/citations?user=aoAn0eAAAAAJ&hl=nl&oi=sra</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=User:Derks047&diff=1634
User:Derks047
2016-01-20T13:41:25Z
<p>Derks047: </p>
<hr />
<div>I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations. I'am also very experienced in de novo genome assembly & annotation.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=User:Derks047&diff=1633
User:Derks047
2016-01-20T13:40:53Z
<p>Derks047: </p>
<hr />
<div>I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations.<br />
<br><br />
I also have a lot of experience in genome assembly & annotation.</div>
Derks047
https://wiki.anunna.wur.nl/index.php?title=User:Derks047&diff=1632
User:Derks047
2016-01-20T13:40:41Z
<p>Derks047: Created page with "I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations. I also have a lot of experience in genome assembly & annotation."</p>
<hr />
<div>I'm a PhD student at ABGC, my project is about the detection of deleterious alleles in livestock populations.<br />
I also have a lot of experience in genome assembly & annotation.</div>
Derks047