Xenopus Genome Browser

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Revision as of 12:11, 5 June 2014 by TaejoonKwon (Talk | contribs)

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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 (JBrowse-1.11.4 for the current version).


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/.

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 [1]).

Index for gene name search

bin/generate-names.pl -v

How to use

I think it is very straightforward to use.

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