J browse WormBase Workshop International Worm Meeting 2015
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- 1. A New Genome Browsing Tool at WormBase Scott Cain
scott@scottcain.net WormBase Developer GMOD Project
Coordinator
- 2. Old Genome Browser (GBrowse) Has been around a LONG TIME (it
looks a little like the 90s). Can have issues dealing with newer
data types (no support for VCF, BAM can be quite slow). Has reached
end of development. Considerable hassle to maintain.
- 3. New Genome Browser (JBrowse) Next Gen genome browser in the
GMOD project. Uses JavaScript/AJAX to provide a very interactive,
speedy experience. Image rendering takes place in the web browser
rather than on a server (speedy for you, smaller servers for
us).
- 4. Navigation (show movie)
- 5. Data Manipulation File menu Open (local/remote) Combination
Tracks Sequence Search
- 6. Open Supports BAM, BigWig/Bed, Indexed VCF and GFF3 Supports
local open, i.e., it will open files without uploading them to a
server (so it is FAST) Fetching by URL from web/ftp (so can use
Google Drive, DropBox, etc)
- 7. Combination Tracks After selecting Create Combination Track,
simply drag the two tracks together that you want to combine. Use
set operations to combine (intersection, union, subtraction,
etc)
- 8. Sequence Search Create a persistent track that will show you
when reference sequence matches a pattern. Can be strand specific
Can use regular expressions Can search DNA or translated amino acid
sequence
- 9. Other Niceties Pin to top makes a track sticky at the top
(wont scroll away) Download track data Create a URL that you can
email, post, etc. Full page button removes WormBase header/footer
giving you the whole web page for genome browsing.
- 10. Wrap up Much thanks to Ian Holmes (UC Berkeley) and his
group, particularly Rob Buels, and Colin Diesh in Chris Elsiks
group (U Missouri). Poster 953A (Thursday, 9:00-10:30PM) The new
genome browser is available at http://jbrowse.wormbase.org/
(redirects to main WormBase site). I tend to hang out on IRC
(##worms and #gmod at freenode.net), and of course you can always
send email to help@wormbase.org or me directly at
scott@scottcain.net. PLEASE feel free to make suggestions for
improvements!