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