Dear all:

Recently, I run cufflink in galaxy on the internet. I want to compare two samples, However, I found no transcript or gene passed the significant level, even many of them have large FPKM in one sample and 0 FPKM in another sample.

Any thoughts?

Below is my cufflink process:

I have four samples belong to two group. the test have three samples, and the control has one sample.

First, using accept_hit.bam from tophat, I run cufflink without annotation on each sample.

Then, for the four "gtf" files from four samples, I run cuffcompare to combine these transcript and compare to the annotation genome. However, at this step, I found the transcript accuracy is very low.
See one example:
Missed exons:    10673/11776 ( 90.6%)
    Wrong exons:    1254/2007 ( 62.5%)
 Missed introns:    8529/8637 ( 98.7%)
  Wrong introns:    2/5 ( 40.0%)
 Missed loci:    0/504 (  0.0%)
  Wrong loci:    1248/2002 ( 62.3%)

at last, I run cufdiff between this two group sample.

Thank you.