Would you be able to submit this as a bug report?
On 2/10/14 11:07 AM, Janice Patterson wrote:
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
Error: duplicate GFF ID 'CUFF.1.1' encountered!
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
Why did turning on bias correction and providing cufflinks with a
fasta reference file making cuffmerge fail?
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