cuffcompare only generates .gtf.tmap and .gtf.refmap?

[julio514]

Hi all,

I've been able to run a tophat/cufflinks with no prob. However, when I run cuffcompare, it only gives me the .gtf.tmap and .gtf.refmap files with no <outprefix>, <outprefix>combined.gtf, and <outprefix>.tracking files.

My cuffcompare command looks something like this.

cuffcompare -V -r blabla.gff -s blabla.fa tanscripts_1.gtf transcripts_2. gtf and so on...

Anyone ever encountered this issue?
Cheers,

[hibachings2013]

i just got the same situation. have you resolved this problem??

[julio514]

Unfortunately no. I haven't try to solve this issue since a couple of months though. I'm wondering if it has to do with the fact that I am comparing samples with no replicates... Are you trying Cufcompare with replicates?

[hibachings2013]

yes, data i use have replicates.

[hibachings2013]

and each of the lanes correspond to a pooled sample of 5-6 replicates.