JBrowse: Difference between revisions

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m (<source> to <pre> to fix code blocks)
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Run the setup script to install perl dependencies and required modules
Run the setup script to install perl dependencies and required modules


<source lang='bash'>
<pre>
unzip JBrowse-1.12.0.zip
unzip JBrowse-1.12.0.zip
mv JBrowse-1.12.0/* $PWD
mv JBrowse-1.12.0/* $PWD
./setup.sh
./setup.sh
</source>
</pre>


=== Add reference sequence ===
=== Add reference sequence ===
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Example code for chicken genome
Example code for chicken genome


<source lang='bash'>
<pre>
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa
</source>
</pre>


To remove tracks use following command:
To remove tracks use following command:


<source lang='bash'>
<pre>
bin/remove-track.pl -D --trackLabel 'trackname'
bin/remove-track.pl -D --trackLabel 'trackname'
</source>
</pre>


===Add annotation files (GFF/BED)===
===Add annotation files (GFF/BED)===
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Add gene features:
Add gene features:


<source lang='bash'>
<pre>
bin/flatfile-to-json.pl --key "Genes" --type gene --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3
bin/flatfile-to-json.pl --key "Genes" --type gene --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3
</source>
</pre>


Add corresponding transcripts:
Add corresponding transcripts:


<source lang='bash'>
<pre>
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
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
</source>
</pre>


===Alignment tracks (BAM)===
===Alignment tracks (BAM)===


You can load single BAM-files by following command:
You can load single BAM-files by following command:
<source lang='bash'>
<pre>
bin/add-bam-track --label <label> --bam_url <url>
bin/add-bam-track --label <label> --bam_url <url>
</source>
</pre>


To load multiple BAM files present in a certain directory use:
To load multiple BAM files present in a certain directory use:
<source lang='bash'>
<pre>


for bam in /<dir>*.bam; do
for bam in /<dir>*.bam; do
Line 90: Line 90:


done
done
</source>
</pre>


Make sure the BAM file can be read by a everybody if not use:
Make sure the BAM file can be read by a everybody if not use:
<source lang='bash'>
<pre>
chmod +r <BAM_file>
chmod +r <BAM_file>
</source>
</pre>


Make sure that all directoryies in the full path of the BAMfile are executable:
Make sure that all directoryies in the full path of the BAMfile are executable:
<source lang='bash'>
<pre>
chmod +x <dir>
chmod +x <dir>
</source>
</pre>


===Variant tracks (VCF)===
===Variant tracks (VCF)===
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To load a VCF file in JBrowse make sure the file is gzipped and indexed
To load a VCF file in JBrowse make sure the file is gzipped and indexed


<source lang='bash'>
<pre>
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz
tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz


Line 117: Line 117:
       "type" : "HTMLVariants"
       "type" : "HTMLVariants"
     } ' | bin/add-track-json.pl data/trackList.json
     } ' | bin/add-track-json.pl data/trackList.json
</source>
</pre>


===Wiggle/BigWig tracks (WIG)===
===Wiggle/BigWig tracks (WIG)===


You can load single BigWig-files by following command:
You can load single BigWig-files by following command:
<source lang='bash'>
<pre>
bin/add-bw-track --label <label> --bw_url <url>
bin/add-bw-track --label <label> --bw_url <url>
</source>
</pre>


===Evidence tracks===
===Evidence tracks===
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Evidence tracks can be loaded in bed, gff and gbk format using  
Evidence tracks can be loaded in bed, gff and gbk format using  


<source lang='bash'>
<pre>
bin/flatfile-to-json.pl
bin/flatfile-to-json.pl
</source>
</pre>


Examples are given above.
Examples are given above.

Revision as of 15:47, 15 June 2023

Typical commands used to set up a JBrowse

Author: Martijn Derks

Install JBrowse

Download the latest JBrowse here: http://jbrowse.org/

Make a directory in /cm/shared/apps/jbrowse/ for your species of interested (e.g. mkdir Cyprinus_carpio). 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). Run the setup script to install perl dependencies and required modules 

unzip JBrowse-1.12.0.zip
mv JBrowse-1.12.0/* $PWD
./setup.sh

Add reference sequence

Example code for chicken genome 

bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa

To remove tracks use following command: 

bin/remove-track.pl -D --trackLabel 'trackname'

Add annotation files (GFF/BED)

Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html

Add gene features: 

bin/flatfile-to-json.pl --key "Genes" --type gene --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3

Add corresponding transcripts: 

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

Alignment tracks (BAM)

You can load single BAM-files by following command: 

bin/add-bam-track --label <label> --bam_url <url>

To load multiple BAM files present in a certain directory use: 


for bam in /<dir>*.bam; do
        ln -s $bam track_symlinks/ ## Make symlinks from the BAM files
        ln -s $bam.bai track_symlinks/ ## Make symlinks to the BAM index files
        tissue=`echo $bam | rev | cut -c 5- | cut -d'/' -f1 | rev` ## USe the name of the file without .bam as trackLabel
        
        ## Add BAM in alignment mode (Alignments2)
        echo '{
                "label" : "'${tissue}'_alignment",
                "key" : "'${tissue}'_alignment",
                "storeClass" : "JBrowse/Store/SeqFeature/BAM",
                "urlTemplate" : "../track_symlinks/'${tissue}'",
                "category" : "3. RNA-seq alignments",
                "type" : "Alignments2"
        }' | bin/add-track-json.pl data/trackList.json

        ## Add BAM in coverage mode (SNPCoverage)
        echo '{
                "label" : "'${tissue}'_coverage",
                "key" : "'${tissue}'_coverage",
                "storeClass" : "JBrowse/Store/SeqFeature/BAM",
                "urlTemplate" : "../track_symlinks/'${tissue}'",
                "category" : "3. RNA-seq alignments",
                "type" : "SNPCoverage"
        }' | bin/add-track-json.pl data/trackList.json

done

Make sure the BAM file can be read by a everybody if not use: 

chmod +r <BAM_file>

Make sure that all directoryies in the full path of the BAMfile are executable: 

chmod +x <dir>

Variant tracks (VCF)

To load a VCF file in JBrowse make sure the file is gzipped and indexed 

tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz

echo ' {
       "label" : "Gallus_gallus_incl_consequences",
       "key" : "Gallus_gallus_incl_consequences",
       "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
       "urlTemplate" : "../../ensembl_data/VCF/Gallus_gallus_incl_consequences.vcf.gz",
       "category" : "2. Variants",
       "type" : "HTMLVariants"
     } ' | bin/add-track-json.pl data/trackList.json

Wiggle/BigWig tracks (WIG)

You can load single BigWig-files by following command: 

bin/add-bw-track --label <label> --bw_url <url>

Evidence tracks

Evidence tracks can be loaded in bed, gff and gbk format using 

bin/flatfile-to-json.pl

Examples are given above.

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