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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. -
cuffcompare fails to produce gtf and tracking
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:
But I dont know why that would be? Any ideas?Code:Total union super-loci across all datasets: 281187 (0 multi-transcript, ~0.0 transcripts per locus)
Chris
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