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Old 05-15-2012, 10:03 AM   #1
apratap
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Location: Bay Area

Join Date: Jan 2009
Posts: 58
Smile Question: Advice : building transcript models using cufflinks

Hi Guys

Keeping it short I want to know which is a better approach for building transcripts models using cufflinks.

If I have an older set of gene models (as a .gtf file) for a species and some new RNA-Seq data, which approach is recommended:

Use RABT (reference annotation based transcript) assembly by providing the gene models to Cufflinks, or
Build the transcriptome de-novo using Cufflinks and then use Cuffmerge to merge the new model with the older one.
Our goal is to improve the existing gene models using new RNA-Seq data.

PS: cross posted on biostar :
http://www.biostars.org/post/show/44...ing-cufflinks/

Thanks!

-Abhi
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Old 10-09-2012, 05:33 PM   #2
secda1
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Hi apratap,

I am also interested in that, do you have any updates on which approach works best ?


Cheers

David
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