cuffdiff output

[kasutubh]

Hi everyone,

I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the gene_id and gene columns in the output files of cuffdiff. Also all the other files except isoform_exp.diff, isoform.FPKM_tracking are blank. When I specify file into the cummeRbund, I get following output,
CuffSet instance with:
2 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS
What might be the problem here? I would really appreciate any help in this regard.
Thanks in advance!

[jp.]

did you get solution? I got same and psoted here :

http://seqanswers.com/forums/showthread.php?p=112110#post112110

may expect your view ?
Thank you

Hi everyone,

I want to analyze data using cummeRbund but I'm having problem with cuffdiff output. I don't get any entries in the gene_id and gene columns in the output files of cuffdiff. Also all the other files except isoform_exp.diff, isoform.FPKM_tracking are blank. When I specify file into the cummeRbund, I get following output,
CuffSet instance with:
2 samples
0 genes
0 isoforms
0 TSS
0 CDS
0 promoters
0 splicing
0 relCDS
What might be the problem here? I would really appreciate any help in this regard.
Thanks in advance!