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post-assembly_analysis:banana_slug_genome_browser [2010/03/31 02:24] galt |
post-assembly_analysis:banana_slug_genome_browser [2015/07/28 06:05] (current) ceisenhart ↷ Page moved from banana_slug_genome_browser to post-assembly_analysis:banana_slug_genome_browser |
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- | * [[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. For those who know how to set up custom track hubs, the link is here. **If it is your first time setting up a custom track hub, follow the instructions for 'Mounting the banana slug track hub' below!** |
- | * [[http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation|Minimal Browser Install]] instructions are on the ucsc genomewiki. | + | |
- | * [[http://hgdownload.cse.ucsc.edu/admin/jksrc.zip|Source Code]] provides kent source zip. | + | http://hgwdev-ceisenhart.cse.ucsc.edu/~ceisenhart/hubs/bananaSlug/hub.txt |
- | * kent/src/product/README* has documentation on configuring and using the UCSC Genome Browser. | + | |
- | * 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. | + | Currently the following assemblies are supported; |
+ | |||
+ | ABySS | ||
+ | |||
+ | SOAP | ||
+ | |||
+ | Discovar //de novo// | ||
+ | |||
+ | Mitochondrial | ||
+ | |||
+ | |||
+ | ===== Mounting the banana slug track hub ===== | ||
+ | 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 which can be used as normal. | ||
+ | |||
+ | =====Creating a new track hub===== | ||
+ | To setup a custom track hub follow the instructions here. | ||
+ | |||
+ | **Note the banana slug track hub has already been created.** These are the instructions that were used to create it the first time, it can be accessed using the instructions above. | ||
+ | |||
+ | https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html | ||
+ |