This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
post-assembly_analysis:banana_slug_genome_browser [2010/03/31 02:29] galt |
post-assembly_analysis:banana_slug_genome_browser [2015/05/23 19:06] 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===== |
- | * [[http://genome.ucsc.edu/admin/mirror.html|Mirroring the UCSC Genome Browser]] shows procedures for setting up a UCSC Genome Browser site. Although we are not trying to set up a mirror site, this still contains valuable configuration information. | + | Currently the banana slug genome is supported as a private track hub. |
- | * [[http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation|Minimal Browser Install]] instructions are on the ucsc genomewiki. | + | |
- | * [[ http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database|Building a new genome database]] on the ucsc genomewiki. | + | http://hgwdev-ceisenhart.cse.ucsc.edu/~ceisenhart/hubs/bananaSlug/hub.txt |
- | * [[http://hgdownload.cse.ucsc.edu/admin/jksrc.zip|Source Code]] provides kent source zip. | + | |
- | * kent/src/product/README* has documentation on configuring and using the UCSC Genome Browser. | + | The entire Ariolimax dolichophallus mitochondrial genome seems to be up on the browser in three contigs! Hopefully tracks will be made soon. |
- | * Internally, the Browser staff uses makeGenome.pl to automate much of the initial build of a browser for a new assembly. The kent source contains that script and other scripts that it calls. | + | |
+ | 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, | ||
+ | |||
+ | 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. |