Why would be de novo gene assembly from RNA-seq data useful?

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6.5 years ago

Yugalee • 0

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?

de novo RNA-Seq • 1.5k views

ADD COMMENT • link updated 6.4 years ago by Biostar 20 • written 6.5 years ago by Yugalee • 0

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

ADD REPLY • link 6.5 years ago by Nicolas Rosewick 11k

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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 REPLY • link 6.5 years ago by jeremias.br ▴ 10

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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 REPLY • link 6.5 years ago by Kevin Blighe 87k

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