Advice : Building Transcript Models Using Cufflinks
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Entering edit mode
12.1 years ago
Abhi ★ 1.6k

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

rna-seq cufflinks transcriptome • 5.8k views
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Entering edit mode

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.

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