Question: How to get / create GFF files for Cufflinks for Zebra Finch genome (taeGut2) on Galaxy ?
0
gravatar for chaoyuan
21 months ago by
chaoyuan80
chaoyuan80 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 • 855 views
ADD COMMENTlink modified 21 months ago by Mo Heydarian800 • written 21 months ago by chaoyuan80
0
gravatar for Mo Heydarian
21 months ago by
Mo Heydarian800
United States
Mo Heydarian800 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 COMMENTlink written 21 months ago by Mo Heydarian800
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 119 users visited in the last hour