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.