Dear Jeremy,
 
Thanks.
 
I am sorry for sending mutiple emails. I will email only once next time.
 
Thank you.
 
Best regards,
Crystal
 



CC: galaxy-user@lists.bx.psu.edu; j...@bx.psu.edu; dbsc...@nus.edu.sg
From: jeremy.goe...@emory.edu
To: crysta...@live.com.my
Subject: Re: Cufflinks with reference annotation and without reference 
annotation
Date: Wed, 17 Aug 2011 14:17:26 -0400

Crystal,


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.


Good luck,
J.




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. Thanks.
 
 
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 Approach 2.
 
Can I get advice on this? 
 
 
Thank you.
 
Best regards,
Crystal
<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>
                                          
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