JBrowse: Difference between revisions
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Data can be downloaded from the Ensembl FTP site: http://www.ensembl.org/info/data/ftp/index.html | 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 "Gene spans" --className feature5 --type gene --noSubfeatures --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/gg_test.gff3 | |||
Revision as of 15:40, 28 January 2016
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/
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:
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