Question: Why would be de novo gene assembly from RNA-seq data useful?
gravatar for Yugalee
3.1 years ago by
Yugalee0 wrote:

I've read some papers where researchers try to assembly genes by just using RNA-seq data. Why would this be useful? Why not just map the RNA-seq to the genome and then quantify and detect genes?

rna-seq de novo • 944 views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 3.1 years ago by Yugalee0

The first application is when you don't have a reference genome to align on.

ADD REPLYlink written 3.1 years ago by Nicolas Rosewick9.2k

As mentioned by Nicolas there are many situations where a good reference is not available. This is especially true in non model organisms. In many cases it might be possible to map to a closely related reference but you will miss novel genes. So de novo assembly is also usefull to detect those novel genes.

ADD REPLYlink written 3.1 years ago by jeremias.br10
  • Where no reference transcriptome or genome is available (Nicolas)
  • To search for novel genes/transcripts, including non-coding RNAs (jeremias)
  • New splice isoforms of already identified genes (or the newly identified transcripts)
  • To search for evidence of fusion-genes
ADD REPLYlink written 3.1 years ago by Kevin Blighe67k
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