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Question: Use novel genome gene annotation file with cufflink
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gravatar for christine.hornlein
4.5 years ago by
christine.hornlein • 0
European Union
christine.hornlein • 0 wrote:

Hi,

I am trying to link my gene annotation file (gff) to Cuffcompare. However the gff file does not show up as a possible choice and the program asks for gtf. I want to use a novel cyanobacteria genome which cannot be found on the net as gtf file yet. I created my own gff file of the annotations with Geneious. Can someone help me with this? How can I convert gff into gtf.

Thanks

Christine
rna-seq • 1.4k views
ADD COMMENT • link •
modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by christine.hornlein • 0
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gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool accepts gtf or gff3. It is much easier to convert gff to gtf (gff3 has a different model that is not single line oriented).

Here is a link with help to the specification for both. You may not be able to do all of the transformations within Galaxy, but some simple text editing (unix or other) seems possible.

Start here, the other two are below:
https://wiki.galaxyproject.org/Learn/Datatypes#GFF

Thanks! Jen, Galaxy team
ADD COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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