Difference between revisions of "JBrowse"
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* The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface. | * The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface. | ||
* The new official JBrowse [http://gmod.org/wiki/JBrowse_FAQ FAQ]. | * The new official JBrowse [http://gmod.org/wiki/JBrowse_FAQ FAQ]. | ||
| + | * Using JBrowse will mean knowing your file formats, so [https://genome.ucsc.edu/FAQ/FAQformat.html here] is UCSC's definitions. | ||
Revision as of 16:48, 20 June 2017
Contents
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 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
Links
- The 2016 Genome Biology paper describing JBrowse, with a good description of the user interface.
- The new official JBrowse FAQ.
- Using JBrowse will mean knowing your file formats, so here is UCSC's definitions.
