cuffcompare fails to produce gtf and tracking

[chrisbala]

Hi All,

I've just run into a problem.

I've mapped reads with tophat, then run cufflinks to qauntify.

Now I'm using cuffcompare to 'compare' the gtf from cufflinks with a ref annotation. Only 2 of the 4 expected output files are being produced: The .loci, and the primary output. No gtf and no tracking files are produced.

The problem seems to be that at the end of the output file I have this:

Total union super-loci across all datasets: 281187 
  (0 multi-transcript, ~0.0 transcripts per locus)

But I dont know why that would be? Any ideas?

Chris

[chrisbala]

nevermind, i think i got it ... i think ... think I need at least 2 gtfs to compare? the trouble is that is not exactly what I want to do. I jsut want to reconcile the cufflinks gtf with the ensembl annotation.