Question: Re: Cufflinks With Reference Annotation And Without Reference Annotation
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Crystal Goh • 10 wrote:
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; jen@bx.psu.edu; dbschak@nus.edu.sg
To: crystal86@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.
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.
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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modified 7.3 years ago
by
Jeremy Goecks • 2.2k
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written
7.3 years ago by
Crystal Goh • 10
