Difference between revisions of "JBrowse"
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=Introduction= | =Introduction= | ||
| − | + | JBrowse is a genome browser which is web-based (as opposed to genome browsers such as Artemis and IGV which are stand-alone applications). | |
| + | |||
| + | It was designed as a fast version of GBrowse,the well-known web-based UCSD genome browser. The key to its speed is Javascript language in which it was developed and which explains the '''J''' in its name. | ||
= Using = | = Using = | ||
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* Beside the magnifying glass icon, one can just the scaffolds one would liek seelcted as main reference sequence. | * Beside the magnifying glass icon, one can just the scaffolds one would liek seelcted as main reference sequence. | ||
| − | = | + | = Installation notes = |
* Available as subdir within apache root dir | * Available as subdir within apache root dir | ||
Revision as of 09:26, 16 June 2017
Introduction
JBrowse is a genome browser which is web-based (as opposed to genome browsers such as Artemis and IGV which are stand-alone applications).
It was designed as a fast version of GBrowse,the well-known web-based UCSD genome browser. The key to its speed is Javascript language in which it was developed and which explains the J in its name.
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.
Installation notes
- 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
