JBrowse
Typical commands used to set up a JBrowse
Author: Martijn Derks
- JBrowse is available for multiple species:
- Users are free to add usefull commands to this tutorial
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
<source lang='bash'> unzip JBrowse-1.12.0.zip cd JBrowse-1.12.0 ./setup.sh </source>
Add reference sequence
Example code for chicken genome
<source lang='bash'> bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa </source>
To remove tracks use following command:
<source lang='bash'> bin/remove-track.pl -D --trackLabel 'trackname' </source>
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:
<source lang='bash'> 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 </source>
Add corresponding transcripts:
<source lang='bash'> 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>
Alignment tracks (BAM)
You can load single BAM-files by following command: <source lang='bash'> bin/add-bam-track --label <label> --bam_url <url> </source>
To load multiple BAM files present in a certain directory use: <source lang='bash'>
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 </source>
Make sure the BAM file can be read by a everybody if not use: <source lang='bash'> chmod +r <BAM_file> </source>
Make sure that all directoryies in the full path of the BAMfile are executable: <source lang='bash'> chmod +x <dir> </source>
Variant tracks (VCF)
To load a VCF file in JBrowse make sure the file is gzipped and indexed
<source lang='bash'> 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
</source>
Wiggle/BigWig tracks (WIG)
You can load single BigWig-files by following command: <source lang='bash'> bin/add-bam-track --label <label> --bam_url <url> </source>
To load multiple BAM files present in a certain directory use: <source lang='bash'>
for bw in /lustre/nobackup/WUR/ABGC/shared/Chicken/Ensembl_Rna_Seq/*.bw; do
ln -s $bw track_symlinks/
tissue=`echo $bw | rev | cut -c 8- | cut -d'/' -f1 | rev`
echo '{
"label" : "'${tissue}'_BWcoverage",
"key" : "'${tissue}'_BWcoverage",
"storeClass" : "BigWig",
"urlTemplate" : "../track_symlinks/'${tissue}.bam.bw'",
"category" : "3. RNA-seq alignments",
"type" : "JBrowse/View/Track/Wiggle/XYPlot",
"variance_band" : true
}' | bin/add-track-json.pl data/trackList.json
done </source>
Make sure the BAM file can be read by a everybody if not use: <source lang='bash'> chmod +r <BAM_file> </source>
Make sure that all directoryies in the full path of the BAMfile are executable: <source lang='bash'> chmod +x <dir> </source>
Evidence tracks
Evidence tracks can be loaded in bed, gff and gbk format using
<source lang='bash'> bin/flatfile-to-json.pl </source>
Examples are given above.