Question: Adding a custom genome to Galaxy
0
gravatar for westcott
13 months ago by
westcott10
westcott10 wrote:

My reference genome is not available. It is a recent publication. How do I go about adding it?

Paper: http://www.pnas.org/content/114/21/E4296.full Data is in SI and at Phytozome:http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Czofingiensis

ADD COMMENTlink modified 13 months ago • written 13 months ago by westcott10
1
gravatar for westcott
13 months ago by
westcott10
westcott10 wrote:

Thanks for the quick reply. I did upload it to my history, however when I specify tophat to use my reference genome in the workflow editor, it resets to the human genome when I go to run it. I assumed the Galaxy instance had some constraint on using built in genomes for tophat. If that isn't the case, I don't understand the problem.

ADD COMMENTlink written 13 months ago by westcott10

Thanks for explaining the usage. If you are setting the use of the custom genome in the workflow editor, then it should be promoted to a Custom Build first. It will then be in the same listing as the natively indexed genome builds. How to do that is on the link above.

UPDATE: Tophat has been deprecated at http://usegalaxy.org. Please use HISAT instead. The change was made yesterday and the details are here: https://biostar.usegalaxy.org/p/23300/

Thanks! Jen, Galaxy team

ADD REPLYlink modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Upload the fasta version of the genome to Galaxy and use it as a Custom reference genome. This is how: https://galaxyproject.org/learn/custom-genomes/

Any data approaching or over 2 GB should be loaded using FTP: https://galaxyproject.org/support/loading-data/

Thanks, Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k
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