Cuffmerge Error
0
0
Entering edit mode
11.3 years ago
GPR ▴ 390

Hello,

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.

    [FAILED]

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.

• 3.5k views
ADD COMMENT
0
Entering edit mode

I would suggest you to use gtf file from Ensembl.

ADD REPLY

Login before adding your answer.

Traffic: 1543 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6