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

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.
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

Reply via email to