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Old 05-25-2010, 05:56 AM   #5
Cole Trapnell
Senior Member
Location: Boston, MA

Join Date: Nov 2008
Posts: 212

Originally Posted by PFS View Post
Thanks! I will do that.

Just out of curiosity, why in the cufflinks output files *_genes.expr (which reports the gene-level coordinates and expression values), sometimes I get more than one row for the same gene? It's like in some cases (noncoding exons??) the FPKM values from the transcripts corresponding to the same gene do not get summed, although the transcripts are assigned to the same gene.

Thanks in advance for your help.
This is a known bug in Cufflinks and will be fixed in the next release.
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