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.