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.
Question: Problem with FPKM values
5.1 years ago by
msameet • 30
msameet • 30 wrote:
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