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Old 10-17-2011, 06:42 AM   #3
SEQond
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Location: Italy

Join Date: Jul 2010
Posts: 27
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Reply issue 1.
Yes I did use a GTF annotation file I had already created. I used the -G
-G/--GTF <reference_annotation.(gtf/gff)> Tells Cufflinks to use the supplied reference annotation (a GFF file) to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.


I will check what --compatible-hits-norm returns coupled with the -G option and will get back to you.

Reply issue 2.
Related to the multiple comparisons in one--> What I did was to run cuffdiff separetely for each pair. I did try to do 4 comparisons at once at some point by putting the control as the first case in cuffdiff, but the software returned only the first comparison and not the rest 3.
I ll check again if there is a way around this.


New Question, issue 3, possibly related to issue 1.
In the way I am doing the analysis , I am getting a result of multiple NMs per XLOC

What I would prefer is a single NM per line
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