Question: How to get / create GFF files for Cufflinks for Zebra Finch genome (taeGut2) on Galaxy ?
gravatar for chaoyuan
2.1 years ago by
chaoyuan80 wrote:


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 ?


gff annotation galaxy cufflinks • 972 views
ADD COMMENTlink modified 2.1 years ago by Mo Heydarian830 • written 2.1 years ago by chaoyuan80
gravatar for Mo Heydarian
2.1 years ago by
Mo Heydarian830
United States
Mo Heydarian830 wrote:


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:

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Hope this helps!

Cheers, Mo Heydarian, Galaxy Team

ADD COMMENTlink written 2.1 years ago by Mo Heydarian830
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