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.