Introduction

Quick Javascript based Genome Viewer

Using

Like other browsers, JBrowse simply gives a visual way of navigating a set of sequences.

Beside the magnifying glass icon, one can just the scaffolds one would liek seelcted as main reference sequence.

First get reference sequence up

bin/prepare-refseqs.pl --fasta ~/scafs0/eelScaffold32.fa

Then it will accept GFF£ files (not GTF) files as feature tracks with this command:

bin/flatfile-to-json.pl --gff ~/scafs0/aug_s32_lp.gff --trackType CanvasFeatures --trackLabel aug_lp_s32

If you have files in GTF, you can convert them to GFF3 with, say, Agustus' script in the following way:

~/swmake/augustus-3.2.2/scripts/gtf2gff.pl --printExon --gff3 < aug_s320_lp.gtf --out=aug_s320_lp.gff