Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: type of file for reference genome
1
gravatar for namratakumari
4.5 years ago by
namratakumari • 10
United States
namratakumari • 10 wrote:

i want to use a reference genome for tophat. Which type of file the galaxy will recognize?
tophat • 1.2k views
ADD COMMENT • link •
modified 18 months ago by westcott • 10 • written 4.5 years ago by namratakumari • 10
1
gravatar for Dannon Baker
4.5 years ago by
Dannon Baker ♦ 3.7k
United States
Dannon Baker ♦ 3.7k wrote:

Tophat will accept FASTA files for the 'use a genome from the history' option.
ADD COMMENT • link written 4.5 years ago by Dannon Baker ♦ 3.7k
0
gravatar for westcott
18 months ago by
westcott • 10
westcott • 10 wrote:

That doesn't seem to work for me.

ADD COMMENT • link written 18 months ago by westcott • 10

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 REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 168 users visited in the last hour