Question: Advice : building transcript models using cufflinks

[apratap]

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/44961/advice-building-transcript-models-using-cufflinks/

Thanks!

-Abhi

[secda1]

Hi apratap,

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


Cheers

David