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.
Thanks!
-Abhi
1 answer
Either of those approaches may prove useful. I would recommend that you try both and compare the outcome.
Here are some threads with advice you might want to consider first:
Introduction
- RNA-seq pre-processing before de novo transcriptome assembly
- Is there any reason to do de novo transcript assembly if a reference is available?
- Does it makes sense to assemble all my RNA-Seq samples as though they were one?
- de novo small RNA transcriptome assembly for non-model species?
Tool recommendation
Interpretation, post-processing, and applications
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Malachi Griffith
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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.