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post-assembly_analysis:banana_slug_genome_browser [2015/05/16 02:15] ceisenhart |
post-assembly_analysis:banana_slug_genome_browser [2015/07/16 18:10] ceisenhart Major changes under way, please let me finish before doing more |
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- | =====Banana slug genome browser===== | + | ======Banana slug genome browser====== |
- | Currently the banana slug genome is supported as a private track hub. | + | 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, just follow the instructions below! |
http://hgwdev-ceisenhart.cse.ucsc.edu/~ceisenhart/hubs/bananaSlug/hub.txt | 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. | + | Currently the following assemblies are supported; |
- | 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 there is data on the banana slug hub for the following teams; | + | ABySS |
SOAP | SOAP | ||
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Discovar //de novo// | Discovar //de novo// | ||
- | ==== Setup and viewing ==== | + | Mitochondrial |
+ | |||
+ | |||
+ | ==== Mounting the banana slug track hub ==== | ||
To view the banana slug data please go to | To view the banana slug data please go to | ||
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http://hgwdev-ceisenhart.cse.ucsc.edu/~ceisenhart/hubs/bananaSlug/hub.txt | 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. | + | 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 | ||
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