post-assembly_analysis:banana_slug_genome_browser
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post-assembly_analysis:banana_slug_genome_browser [2010/03/31 02:29] galt |
post-assembly_analysis:banana_slug_genome_browser [2015/05/27 20:25] ceisenhart |
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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. |
| - | * [[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 default contig names are often wrong, the correct names 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// | ||
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| + | Mitochondrial | ||
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| + | |||
| + | ==== 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 | ||
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| + | https://genome.ucsc.edu/cgi-bin/hgGateway | ||
| + | |||
| + | and click the 'track hubs' button | ||
| + | |||
| + | {{ ::firstbrowsershot.png |}} | ||
| + | |||
| + | next navigate to the 'my hubs' tab | ||
| + | |||
| + | {{ ::secondbrowsershot.png |}} | ||
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| + | Paste the url provided, | ||
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| + | 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. | ||
post-assembly_analysis/banana_slug_genome_browser.txt · Last modified: 2015/07/28 06:05 by ceisenhart
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