View source for JBrowse

=== Typical commands used to set up a JBrowse === 

Author: Martijn Derks

* JBrowse is available for multiple species:
** https://jbrowse.hpcagrogenomics.wur.nl/pig/
** https://jbrowse.hpcagrogenomics.wur.nl/chicken/
** https://jbrowse.hpcagrogenomics.wur.nl/cattle/
** https://jbrowse.hpcagrogenomics.wur.nl/turkey/
* Users are free to add usefull commands to this tutorial

=== Install JBrowse ===

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

Run the setup script to install perl dependencies and required modules

<source lang='bash'>
unzip JBrowse-1.12.0.zip
./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/gg_test.gff3
</source>