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
6.0 years ago by
msameet • 40
msameet • 40 wrote:
ADD COMMENT • link •
Please log in to add an answer.
Powered by Biostar version 2.3.0
Traffic: 842 users visited in the last hour