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--- post-assembly_analysis:banana_slug_genome_browser [2010/03/31 02:07]
galt created
+++ post-assembly_analysis:banana_slug_genome_browser [2015/05/27 20:24]
ceisenhart
@@ Line 1: / Line 1: @@
-  * [[http://bananadev.cse.ucsc.edu/|Banana Slug Genome Browser]] will have a UCSC genome browser, once we get to the point of having few enough contigs that building a browser makes sense.
+=====Banana slug genome browser=====
+Currently the banana slug genome is supported as a private track hub.
+http://hgwdev-ceisenhart.cse.ucsc.edu/~ceisenhart/hubs/bananaSlug/hub.txt
+The entire Ariolimax dolichophallus mitochondrial genome seems to be up on the browser in three contigs! Hopefully tracks will be made soon.
+The data on the browser is in a VERY EARLY FORMAT. Currently only the 30 longest contig's for each group are supported on the browser.  The contigs are re-named before uploading, and can be viewed by using the 'sequences' button on the browser. Contact Chris Eisenhart to have your team's data put on the browser (ceisenhart@soe.ucsc.edu). Currently the following assemblies are supported;
+ABySS
+SOAP
+Discovar //de novo//
+Mitochondrial
+==== Setup and viewing ====
+To setup a track hub follow the instructions here, the banana slug track hub has already been created. To view it skip to the next section.
+https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
+To view the banana slug data please go to
+https://genome.ucsc.edu/cgi-bin/hgGateway
+and click the 'track hubs' button
+{{ ::firstbrowsershot.png |}}
+next navigate to the 'my hubs' tab
+{{ ::secondbrowsershot.png |}}
+Paste the url provided,
+http://hgwdev-ceisenhart.cse.ucsc.edu/~ceisenhart/hubs/bananaSlug/hub.txt
+into the 'URL' text box and click the 'Add hub' button.  You will be redirected to the banana slug hub.

Banana Slug Genomics

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