Question: Cuffdiff ouput gene expression data
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gravatar for onemoreuser
3.2 years ago by
onemoreuser20
onemoreuser20 wrote:

I run the cuffdiff tool for the first time. My input was something like this:

cuffdiff -p 5 -o ouput_directory -b reference.fa -L A1,A2 -u merged.gtf A1_rep1,A1_rep2 A2_rep1,A2_rep2

Now I'm looking at file "gene_exp.diff" and cufflinks added a 'cufflinks id' for the genes and the transcripts. So one example of a line from my file is:

XLOC_000009 XLOC_000009 Oprk1 1:5578573-5596212 E7 M3 NOTEST 0.125772 0 -inf 0 1 1 no

I see that cufflinks did not wrote the transcript id. Is it possible to know which is the transcript for each line?

Thanks in advance.

ADD COMMENTlink written 3.2 years ago by onemoreuser20
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