Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: How to get / create GFF files for Cufflinks for Zebra Finch genome (taeGut2) on Galaxy ?
0
gravatar for chaoyuan
2.1 years ago by
chaoyuan • 80
chaoyuan • 80 wrote:

Hi,

I'm trying to perform Cufflink on my local instance of Galaxy. I've installed taeGut2 genome from UCSC. I'm having trouble with the GFF files needed for Cufflink, though. I know that I can create a GFF file using the UCSC table browser. However, there are numerous options and I'm very confused about how to get the correct format. Could anyone tell me how to generate a correct GFF file to be used with Cufflink ?

Thanks
gff annotation galaxy cufflinks • 972 views
ADD COMMENT • link •
modified 2.1 years ago by Mo Heydarian ♦ 830 • written 2.1 years ago by chaoyuan • 80
0
gravatar for Mo Heydarian
2.1 years ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hello,

There is a RefSeq annotation for taeGut2 available through the UCSC table browser. You can import this annotation to Galaxy in GTF format with the following parameters:

enter image description here

Hope this helps!

Cheers, Mo Heydarian, Galaxy Team
ADD COMMENT • link written 2.1 years ago by Mo Heydarian ♦ 830
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: 169 users visited in the last hour