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

Strangely for another transcripts I have:
Cufflinks: treat_:0
              untreat_: 0

Cuffdiff:  trat_4.4
          significant: yes

How this can be possible?

I had similar results with other transcripts where one one of the two
had 0 cufflinks, and the other one very high but the cuffdiff come out
with NO TEST or OK but not significant

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