JBrowse is a genome browser which is web-based (as opposed to genome browsers such as Artemis and IGV which are stand-alone applications).
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.
- Available as subdir within apache root dir
First get reference sequence up
bin/prepare-refseqs.pl --fasta ~/scafs0/eelScaffold32.fa
Then it will accept GFF3 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 happen to have files in GTF, you can convert them to GFF3 with, say, Augustus' script in the following way:
~/swmake/augustus-3.2.2/scripts/gtf2gff.pl --printExon --gff3 < aug_s320_lp.gtf --out=aug_s320_lp.gff
BAM files can be incorporated with:
bin/add-bam-track.pl --label WTIPbam --bam_url WTIP_srtd.bam