Ensembl Gtf Cuffmerge Duplicates

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10.1 years ago

andrew.j.skelton73 6.6k

Hi,

I've downloaded two GTF files based on the Ensembl annotation, both of which fail when running gffread -E on them, stating that it cannot parse.

Ensembl Homo Sapiens - http://cufflinks.cbcb.umd.edu/igenomes.html (Using the genes.gtf from the annotation directory) - http://www.ensembl.org/info/data/ftp/index.html (GTF Gene Set)

I've ran the Tophat -> Cufflinks pipes so far, and when getting to the Cuffmerge stage, I get a duplicate entry error. I grepped the annotation GTF file and there doesn't appear to be any duplicates.

If anyone has any suggestions it'd be greatly appreciated, thanks!

duplicates cuffmerge ensembl gtf • 3.0k views

ADD COMMENT • link updated 19 months ago by Ram 43k • written 10.1 years ago by andrew.j.skelton73 6.6k

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what did you grep for?

ADD REPLY • link 10.1 years ago by Phil S. ▴ 700

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Hi Andrew,

I am running cuffmerge using cufflinks v2.1.1 and I ran into the exact same problem you mentioned above. I was wondering if you ever figured it out?

Thanks,
Ellie

ADD REPLY • link updated 19 months ago by Ram 43k • written 8.7 years ago by Jingyue ▴ 70

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Hi Ellie ... This was a long time ago... I honestly can't remember how I went about fixing it. Have you considered using the most up to date GTF, rather than the iGenomes release?? (from here)

ADD REPLY • link 8.7 years ago by andrew.j.skelton73 6.6k

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