Question: Advice : Building Transcript Models Using Cufflinks
3
gravatar for Abhi
6.9 years ago by
Abhi1.5k
United States
Abhi1.5k wrote:

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:

  1. Use RABT (reference annotation based transcript) assembly by providing the gene models to Cufflinks, or
  2. 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.

Thanks!

-Abhi

ADD COMMENTlink modified 8 weeks ago by Biostar ♦♦ 20 • written 6.9 years ago by Abhi1.5k

I have to mention that Augustus with RNA-Seq data and reference as inputs resulted in better gene models for us than Cufflinks. We tested it with Arabidopsis thaliana Col-0. So maybe its also nice to compare gene models from Augustus and Cufflinks with Cuffcompare? Just a thought.

ADD REPLYlink written 6.9 years ago by Arun2.3k
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