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
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.
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
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
