Question: Why would be de novo gene assembly from RNA-seq data useful?
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gravatar for Yugalee
18 months ago by
Yugalee0
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 • 617 views
ADD COMMENTlink modified 17 months ago by Biostar ♦♦ 20 • written 18 months ago by Yugalee0
3

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

ADD REPLYlink written 18 months ago by Nicolas Rosewick7.5k
1

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 18 months ago by jeremias.br10
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  • 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 18 months ago by Kevin Blighe41k
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