Question: rRNA FPKM values all are zero
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gravatar for xusisiyu
6 months ago by
xusisiyu0
xusisiyu0 wrote:

Hi, I have used Tophat2 and cuffdiff to analyze the S.cerevisiae RNA-seq data. But the rRNA FPKM values produced by cuffdiff all are zero although there are many reads that mapped to the rRNA locus. Could you please tell me the possible reason of this? Thank you very much, Best wishes, Siyu

rna-seq fpkm cuffdiff • 150 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson23k • written 6 months ago by xusisiyu0
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Check the "Test status" field of the output. This will inform about what the underlying problem is with the data.

http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#differential-expression-tests

Thanks, Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson23k
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