Help me to sort out Error message for cuffdiff

[Uwe Appelt]

Hi fugenli,

although your setup appears a little different, the "duplicate gff id" issue has been discussed in detail here (start reading from post #7). Unfortunately no fix has been released yet, at least not an official one.

Uwe

[fugenli]

Hi Everyone,

Recently I tried to use cuffdiff to get differential expression lincRNA between two samples. I used mouse gtf file, which I downloaded from ensembl web site. But I could not successfully run it with a few types of errors for gtf file. Here is what I did:

I downloaded mouse gtf file: Mus_musculus.NCBIM37.59.gtf
Generated lincRNA gtf file: grep "lincRNA" Mus_musculus.NCBIM37.59.gtf > Mus_musculus_lincRNA.NCBIM37.59.gtf
Run cuffdiff -p 4 -m 128 Mus_musculus_lincRNA.NCBIM37.59.gtf accepted_hits_s1.sam accepted_hits_s2.sam
Here is the error message: Error: duplicate GFF ID '' (exons found on different strands of chr18). I checked every single exon, there is no one on both strands. After I deleted all records for chr18 and re-run cuffdiff, I got a different error message: Error: duplicate GFF ID '' (or exons too far apart)! I removed any intron with a size of 300000 and re-run it again. I got the same error message. Can anyone help me sort out the problem and tell me what I did wrong and correct them?

Thanks,