align RNA-seq reads to annotated CDS

Question

[Pei]

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!

[GenoMax]

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.