problems with running Cufflinks using Gencode annotation gtf

[arrchi]

Hi there,

Has anybody successfully run Cufflinks with human RNA-Seq data set using Gencode annotation gtf?

I've been trying to run commands like this "cufflinks --num-threads 4 -g ./gencodeV13/gencode.v13.annotation.gtf --min-frags-per-transfrag 0 ./x.bam", but the program stopped after a while, and in the output file, transcripts.gtf, it only has part of Chr1 information.

But I have no problem running tophat with the same annotation file. And x.bam is the output.

And I have no problem using a subset of the Gencode annotation gtf file, for example, the gencode.v13.annotation.exon.gt contains only exon from the annotation file. And I can run "cufflinks --num-threads 4 -g ./gencodeV13/gencode.v13.annotation.exon.gtf --min-frags-per-transfrag 0 ./x.bam" successfully and got information for all chromosomes.

Any idea?

Thanks a lot.

[caballien]

Did you figure this out? I'm having a similar problem. I can use ucscknowngene.gtf with no problems, but when I switched to gencode cufflinks is taking greater than 10x longer and still hasn't finished. I read in another forum that the use of "genes" in gencode in column 3 of the .gtf is causing the issue, and to simply remove those lines. I'm not sure if this is accepted practice.