JBrowse: Difference between revisions

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=== Add reference sequence ===
=== 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
bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa
</source>


===Trim sequences for quality and adapters===
===Trim sequences for quality and adapters===

Revision as of 15:35, 27 January 2016

Typical commands used to set up a JBrowse

Author: Martijn Derks

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>

Trim sequences for quality and adapters