Difference between revisions of "JBrowse"
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JBrowse is a genome browser which is web-based (as opposed to genome browsers such as Artemis and IGV which are stand-alone applications). | 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. | + | 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 = | = Using = | ||
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* Available as subdir within apache root dir | * 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 | bin/prepare-refseqs.pl --fasta ~/scafs0/eelScaffold32.fa | ||
| − | Then it will accept | + | 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 | 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, | + | 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 | ~/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 = | = Links = | ||
* 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. | ||
| + | * JBrowse's configuration guide is [http://gmod.org/wiki/JBrowse_Configuration_Guide here]. | ||
| + | * 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. | ||
Latest revision as of 07:08, 4 August 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 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.
