JBrowse

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 the 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

The very first, or zeroth step can seem somewhat tedious and unnecessary, but it is best to follow it, for completeness sake.

A file called setup.sh exisits in the root directory of the JBrowse (note: not the bin directory where all the other scripts are kept). Run this first.

./setup.sh

Then, 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

However, to get a clean and approachable coverage track in reads per 100bp, you need to use bigWig files, so a prior operation of converting BAM to bigWig (bw) files is necessary using deeptools:

bamCoverage -b reads.bam -o coverage.bw

Then we can go ahead and:

bin/add-bw-track.pl --plot --bw_url ULSINP_srtd_cov.bw --label ULS1INPcov

Probably you will need to edit the trackList.json file to color these.

Adding a bed6+4 file characteristic of MACS2 peak-calling narrowPeak format.

bin/flatfile-to-json.pl --trackLabel WTpeaks --trackType CanvasFeatures --bed data/wtip_pk.npk --clientConfig '{"featureCss": "background-color: #668; height: 8px;"}'

Links

• The 2016 Genome Biology paper describing JBrowse, with a good description of the user interface.
• JBrowse's configuration guide is here.
• The new official JBrowse FAQ.
• Using JBrowse will mean knowing your file formats, so here is UCSC's definitions.