Difference between revisions of "JBrowse"
(Created page with "=Introduction= Quick Javascript based Genome Viewer = Using = Like other browsers, JBrowse simply gives a visual way of navigating a set of sequences. * Beside the magnify...") |
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bin/prepare-refseqs.pl --fasta ~/scafs0/eelScaffold32.fa | bin/prepare-refseqs.pl --fasta ~/scafs0/eelScaffold32.fa | ||
| − | Then it will accept | + | 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 | 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: | ||
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| + | ~/swmake/augustus-3.2.2/scripts/gtf2gff.pl --printExon --gff3 < aug_s320_lp.gtf --out=aug_s320_lp.gff | ||
Revision as of 22:54, 4 May 2016
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.
Install
- Available as subdir within apache root dir
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
