Question: Cuffmerge Error
gravatar for GPR
7.5 years ago by
GPR320 wrote:


I have been running Cufflinks/Cuffmerge/Cuffdiff for quite a while, have updated it several times and never had a problem. I typically use the Refseq genes.gtf file for my analysis but recently have started to use a known-Genes-UCSC.gtf file, which I have downloaded from the UCSC tables and from the MISO website. My problem is that everytime I run TopHat and Cufflinks with known-Genes-UCSC.gtf, I get the following error in Cuffmerge:


Preparing output location ./merged_asm/

Converting GTF files to SAM

[16:14:33] Loading reference annotation.


Error: could not execute gtf_to_sam


I suspect this might have to do with the formatting of the new gtf I have started using? Anybody have suggestions on this? I don't think it has to do with the PATH, because Cuffmerge works perfectly fine with genes.gtf.

Thanks, G.

ADD COMMENTlink written 7.5 years ago by GPR320

I would suggest you to use gtf file from Ensembl.

ADD REPLYlink written 6.2 years ago by Ram160
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