Question: Cuffmerge
gravatar for Janice Patterson
4.4 years ago by
Janice Patterson20 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 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
gff cuffmerge cufflinks rna-seq • 2.2k views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by Janice Patterson20
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Janice, Are you using the public Main Galaxy instance at Would you be able to submit this as a bug report? Thanks, Jen Galaxy team -- Jennifer Hillman-Jackson
ADD COMMENTlink written 4.4 years ago by Jennifer Hillman Jackson25k
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