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Old 04-03-2013, 03:09 PM   #1
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Location: Michigan

Join Date: Mar 2011
Posts: 7
Question Transcripts missing from Cufflinks FPKMtracking file. Run with -G option


I am using Cufflinks with the -G option to get the FPKM values of all transcripts specified in the Ensembl annotation file. But when I look at the isoforms.FPKM_tracking file, I see that some of the transcript ids present in the annotation file are missing from this output file.

It is only a few transcripts (1700 out of approx 190,000 ). But I am curious as to why they are missing.

Many of the transcripts reported in the FPKM tracking file do have 0 FPKM values, so they are probably not missing because they have 0 FPKM. And the missing transcripts don't seem to have any particular trend. They are from all chromosomes in the genome. They include both protein_coding and other types of transcripts. So not sure why they would be missing.

Has anyone else had this same issue? Can I change anything to make those transcripts show up? Or should I just assume their FPKM values to be zero and proceed?

I am using Cufflinks 1.1.0 (I know its a fairly old version, but I don't have privileges to install a newer version on this machine.)

thanks in advance..
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