Xenopus Genome Browser

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On service

How to install

I use JBrowse for this. I have tried to install Gbrowse and UCSC browse before (not fully succeeded), but I believe this is much easier to install/configure/use, especially with short read sequencing data.

First, see the 'Installation' part of current Jbrowse tutorial below. If your web server is correctly configured, all you need to do are (1) download and uncompress the code, and (2) run './setup.sh' in the directory. I am using this browser for various organisms/genome versions, so it would be good to rename the directory of the browser, rather than default name (I used 'XENTR_JGIv80' as directory name).


How to configure

All reference and annotation files that I used to make current X. tropicalis browser are available at http://daudin.icmb.utexas.edu/XENTR_JGIv80/raw/. You can tweak the configuration by editing 'data/trackList.json' file. You can see current trackList.json file for 'XENTR_JGIv80' at http://daudin.icmb.utexas.edu/XENTR_JGIv80/data/trackList.json .

Reference sequences

Next install reference sequence via 'bin/prepare-refseq.pl'.

bin/prepare-refseqs.pl --fasta <my genome fasta file>


Next install gene annotation info using 'bin/flatfile-to-json.pl'.

bin/flatfile-to-json.pl --gff <my gff3 file> --trackLabel <the name of track>

For the record, I made all current GFF3 files using GMAP, after extra clean-up with my script (also available at http://daudin.icmb.utexas.edu/XENTR_JGIv80/raw/clean-gmap_gff.py).

Index for gene name search

bin/generate-names.pl -v

Short read sequencing data

You can present BAM file directly (but should be sorted and indexed using samtool), without converting to bed/wig/bigWig files. Put your *.bam and *bai files in web accessible directory (I created 'bam/ directory at the root of JBrowse for it), and add some lines at 'data/tracks.conf' file. You can see current trackList.json file for 'XENTR_JGIv80' at http://daudin.icmb.utexas.edu/XENTR_JGIv80/data/tracks.conf .

How to use

I think it is very straightforward to use. Several 'non-obvious' things:

  • If you click annotation item, you can see (1)whole genomic region sequence, (2) processed mRNA sequence, (3) exons, and (4) CDS sequences in separate box.
  • Also, you can download genomic sequence of your screen.
    1. Move mouse pointer to 'Reference Sequence' label on the genome browser panel. You can see the extra menu button on the right (arrow). Click it.
    2. The 5th menu is 'Save track data'. Select it, then you can see the menu to save visible region as FASTA file (or you can view it on the browser by choosing 'View' button at bottom).