Question: type of file for reference genome
1
gravatar for namratakumari
3.9 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 • 847 views
ADD COMMENTlink modified 10 months ago by westcott10 • written 3.9 years ago by namratakumari10
1
gravatar for Dannon Baker
3.9 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 3.9 years ago by Dannon Baker3.7k
0
gravatar for westcott
10 months ago by
westcott10
westcott10 wrote:

That doesn't seem to work for me.

ADD COMMENTlink written 10 months ago by westcott10

Custom genome help: https://galaxyproject.org/learn/custom-genomes/

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 http://usegalaxy.org? 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 (galaxy-bugs@lists.galaxyproject.org) for feedback when working at http://usegalaxy.org 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 10 months ago by Jennifer Hillman Jackson24k
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