Question: GTF usage in Cufflinks
0
gravatar for bimbam42
3.9 years ago by
bimbam4210
Switzerland
bimbam4210 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?

 

ADD COMMENTlink modified 3.4 years ago by archana bhardwaj20 • written 3.9 years ago by bimbam4210
0
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k

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 REPLYlink written 3.9 years ago by bimbam4210

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 REPLYlink written 3.9 years ago by Jennifer Hillman Jackson25k
0
gravatar for archana bhardwaj
3.4 years ago by
United States
archana bhardwaj20 wrote:

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

 

 

ADD COMMENTlink written 3.4 years ago by archana bhardwaj20
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