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. Thanks.
After aligning RNA-seq reads with Tophat, I used the Tophat output
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?
<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
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