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Old 09-19-2013, 07:19 AM   #1
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Location: USA

Join Date: Sep 2012
Posts: 130
Default Cufflinks/Cuffdiff different FPKM values for multiple genes at one location

I am doing my first RNA-seq for Drosophila melanogaster (I normally deal with human or mouse data). It turns out there are a lot of fly genes that have identical coordinates as other genes. In other words, the same location has multiple genes assigned to it.

If there are multiple genes that have the same exact coordinates, they should have the same FPKM values. However, running Cuffdiff using a GTF like that does not yield the same values for all genes.

Is there a way to force Cuffdiff to assign the same values to all overlapping genes? I could not find any arguments that may do that. Is there a proper way of dealing with such situations? Do I need to optimize the GTF file? I use the one from iGenomes, which is endorsed by Cufflinks, so it seems like it should be fine.
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