Question: type of file for reference genome
gravatar for namratakumari
4.5 years ago by
United States
namratakumari10 wrote:

i want to use a reference genome for tophat. Which type of file the galaxy will recognize?

tophat • 1.2k views
ADD COMMENTlink modified 18 months ago by westcott10 • written 4.5 years ago by namratakumari10
gravatar for Dannon Baker
4.5 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

Tophat will accept FASTA files for the 'use a genome from the history' option.

ADD COMMENTlink written 4.5 years ago by Dannon Baker3.7k
gravatar for westcott
18 months ago by
westcott10 wrote:

That doesn't seem to work for me.

ADD COMMENTlink written 18 months ago by westcott10

Custom genome help:

The two most common reasons for problems are (both covered in link above):

  • The fasta dataset does not have fasta assigned as the datatype
  • The formatting of the fasta file does not match specification

Other related topics:

If you are still having usage problems after reviewing, please explain with more details about what is not working and where you are using Galaxy (Galaxy Main at Local or Cloud Galaxy? Some other public or private Galaxy?).

If you want to keep your data private, you could also send in a bug report (directly from an error dataset) or shared history link ( for feedback when working at or the issue can be reproduced there. If you send something in, please include a link to this post so we can associate the two.

Thanks, Jen, Galaxy team

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
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