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post-assembly_analysis:banana_slug_genome_browser [2010/03/30 19:29]
galt
post-assembly_analysis:banana_slug_genome_browser [2015/07/27 23:05] (current)
ceisenhart ↷ Page moved from banana_slug_genome_browser to post-assembly_analysis:banana_slug_genome_browser
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 ​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 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://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+Currently ​the following assemblies ​are supported; 
-  * 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.+ 
 +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 
 + 
post-assembly_analysis/banana_slug_genome_browser.1270002591.txt.gz · Last modified: 2010/03/30 19:29 by galt