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align RNA-seq reads to annotated CDS

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
• 2,723 views • link
written by Pei Pei
  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.
• 0 views • link
written by GenoMax GenoMax

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