[galaxy-dev] Cufflinks with reference annotation and without reference annotation
jen at bx.psu.edu
Wed Aug 17 15:02:28 EDT 2011
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.
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On 8/17/11 9:42 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
> 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
> 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,
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