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Question: GTF usage in Cufflinks
0
gravatar for bimbam42
4.1 years ago by
bimbam42 • 10
Switzerland
bimbam42 • 10 wrote:

My problem is that Cufflinks does not recognize the gtf file that I provide. It shows an error that the gff ID is duplicated but I am not using a gff file. How can I set the parameter as gtf so that Cufflinks will use my gtf file?

 
annotation reference gff_ids cufflinks • 1.9k views
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modified 3.6 years ago by archana bhardwaj • 20 • written 4.1 years ago by bimbam42 • 10
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Would you like to share a sample of your file? A bit of the header, maybe a few lines in the middle, and the last 10 or so lines. You can use tools in the "Text Manipulation" tool group to do this quickly.

I have a few ideas about what might be going on, but rather than guess and list all out, let's looks at the actual file and figure it out together. Please include a link to the exact source if at all possible.

Thanks! Jen, Galaxy team

ps: If this has been solved already, just let us know.
ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

I solved the problem. I found out that it is easier to use a gff file that I modify before using it with cufflinks. Cufflinks uses a script to convert gff to gtf:

gffread -E annotation.gff -T -o- | more

My idea war to have EntrezGeneIds instead of GFF ID=genexxx.

Thanks for replaying anyway.

Cheers Jochen

ADD REPLY • link written 4.1 years ago by bimbam42 • 10

Glad resolved! Yes, if the GTF contains dup IDs, they will be picked up by this tool. Is what I wanted to help check, but very happy you were able to discover on own and move forward! Best, Jen, Galaxy team

ADD REPLY • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for archana bhardwaj
3.6 years ago by
archana bhardwaj • 20
United States
archana bhardwaj • 20 wrote:

There is another script available at https://github.com/smarguer/MISC_scripts/blob/master/GFFtoGTF.pl to convert gff to gtf 

 

 
ADD COMMENT • link written 3.6 years ago by archana bhardwaj • 20
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