cuffdiff output

kasutubh

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Join Date: Mar 2010

Posts: 25
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#1

cuffdiff output

03-20-2012, 06:57 PM

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!
Tags: cuffdiff, cummerbund
jp.

Senior Member

Join Date: Jul 2013

Posts: 142
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#2

07-30-2013, 06:46 PM

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

Empty instance in cummeRbund - SEQanswers

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

Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

may expect your view ?
Thank you

Originally posted by kasutubh View Post

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!
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