I am analyzing RNA-seq data and I ran Cufflinks with the genes.gtf as a reference annotation guide, with bias correction using the genome.fa as a reference.

When I subsequently attempt to run cuffmerge on my assembled transcript files, however, I get the following errors, and cuffmerge fails.

Error: duplicate GFF ID 'CUFF.1.1' encountered!
         [FAILED]
Error: could not execute gtf_to_sam

I am using the same genes.gtf file I used for cufflinks. It is the genes.gtf file attained from the Data Libraries provided by galaxy.

I ran Cufflinks on the same data set without bias correction (and therefore a genome.fa file was unnecessary) and no multi-read correct, and subsequent cuffmerge with the same genes.gtf file provided ran just fine.

Why did turning on bias correction and providing cufflinks with a fasta reference file making cuffmerge fail?

Thanks.

Janice Patterson