I am sorry for sending mutiple emails. I will email only once next time.
CC: galaxy-user(a)lists.bx.psu.edu; jen(a)bx.psu.edu; dbschak(a)nus.edu.sg
Subject: Re: Cufflinks with reference annotation and without reference annotation
Date: Wed, 17 Aug 2011 14:17:26 -0400
If you provide a gene annotation to Cufflinks, the transcripts produced will match those
in the annotation exactly. If you assemble without a gene annotation, the transcripts
produced will match the reference in some cases, but, in others, will not match the
reference due to small and/or large errors. Because '=' denotes an exact match
between an assembled transcript and a reference transcript, more '=' are to be
expected when Cufflinks has a gene annotation.
Finally, a couple procedural issues:
*please send questions about analyses and tool usage to the galaxy-user mailing list, not
galaxy-dev or individual developers;
*please do not send duplicate emails as it can confuse our tracking system and slow down
our response rather than speed it up.
On Aug 17, 2011, at 9:14 AM, Crystal Goh wrote:
Hi, I am Crystal. I have some problem with Cuffdiff output. Hope can get some advice.
After aligning RNA-seq reads with Tophat, I used the Tophat output for Cufflinks.
For Cufflinks, I tried two approaches and compared the results:
1st approach: Put zebrafish Ensembl GTF as reference annotation
2nd approach: without reference annotation.
From the output of above 2 approaches, I continued with Cuffcompare
(with reference annotation) and Cuffdiff,
Attached word document is the workflow and
parameters I set for these 2 approaches.
When I compared the output of Cuffdiff between these 2 approaches, a total of 48584
tracking id with class code "=" was observed in trancript FPKM tracking file
from Approach 1, whereas there is only 1248 tracking id with class code '=' from
Approach 2 (I attached transcript FPKM tracking files from approach 1 and 2)
In my opinion, I should observe 48584 tracking id with class code '=' and
additional tracking id with other class codes in transcript FPKM tracking file from
Can I get advice on this?
<Workflow and parameter for 2 approaches.zip><Approach 1 Transcript FPKM tracking
(Cufflinks with reference annotation).zip><Approach 2 Transcript FPKM tracking
(Cufflinks without reference annotation).zip>