JBrowse: Difference between revisions

From HPCwiki
Jump to navigation Jump to search
Line 22: Line 22:


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


===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

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

Trim sequences for quality and adapters