Question: align RNA-seq reads to annotated CDS
gravatar for lin.pei26
3.1 years ago by
lin.pei2670 wrote:

Hi all:

when performed a RNA-seq data processing, we usually align reads to the genome. I just have a simple questions: for species with a good annotation, like human, could one just align RNA-seq reads directly to the annotated CDS to quantify/estimate the abundance of known transcripts ? what is the potential drawback ?

Thanks in advance!

rna-seq • 1.1k views
ADD COMMENTlink written 3.1 years ago by lin.pei2670
  1. You are going to miss genes that were not previously known/annotated (or are not present in the CDS set you used).
  2. Aligners may try to align reads to regions to which they do not belong.
ADD REPLYlink written 3.1 years ago by genomax68k
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