Question: Problem with FPKM values
gravatar for msameet
6.5 years ago by
United States
msameet40 wrote:

I recently did a cuffdiff to estimate differential expression under two different conditions.  I did not have replicates for the data-sets.  I used tophat2 and cuffdiff2 for alignment and differential expression respectively.  However, most strangely, when I viewed the alignment on IGV, I can see four genes where the coverage is decent, but the FPKM table shows a value of zero in both conditions.  Now I should say, that these genes are tandem-ly repeated.  However, when I tried to look for other repeat regions in the genome, they had some FPKM value assigned to it.  I wonder what is going on.

ADD COMMENTlink modified 6.5 years ago by swbarnes29.4k • written 6.5 years ago by msameet40
gravatar for swbarnes2
6.5 years ago by
United States
swbarnes29.4k wrote:

If the reads have a mapping quality of 0, because they are squarely in repeat areas, Cuffdiff might have skipped over it.  Maybe other regions are not quite perfectly repetitive.

ADD COMMENTlink written 6.5 years ago by swbarnes29.4k
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