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
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