Hello Irene,
It may be that the reference annotation GTF file was absent or did not
have content for the transcript in the Cufflinks run that produced the
"0" FPKM results. Then the reference annotation GTF used for Cuffdiff did.
If the Cufflinks documentation about calculations does not alig
dear all these are the cuffdiff outputs for the same transcript/gene
(one isoform only):
transcript differential expression
value1 value2log2fold test stat pvalue
q value significant
18.8175 114.371 2.60357 -2.883580.00393177 0.0630024 no
Dear all,
I have two samples, treated and untreated.
I ran cufflinks and had the following FPKM:
treated: 884532
untreat.: 130247
I then ran cuffdiff and look at the transcript diff. expression values:
treated: 33
untreat.:2.9
significant:yes
Strangely for another transcripts I have the followi
Dear all,
I have two samples, treated and untreated.
I ran cufflinks and had the following:
treated: 884532
untreat.: 130247
I then ran cuffdiff and look ath transcript diff. expression:
treated: 33
untreat.:2.9
significant:yes
Strangely for another transcripts I have:
Cufflinks: treat_:0
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