When doing differential gene analysis, why measuring genes based on exons? Can we measure genes based on CDS?
The purpose of RNA-seq is to measure expression at the transcription level. RNA-seq is neither able nor intended to measure expression at the translation level. Hence exons are relevant and CDSs are not.
RNA-seq allows you to measure lots of interesting and important transcripts that don't code for proteins at all.
Even if your interest was limited to protein coding genes, and to likely protein expression, you would still need to measure RNA level expression in order to predict protein expression, and the exons give you the best means to do that.
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Are you asking if it's OK to exclude the UTRs from the gene model when quantifying genes from reads? Why would you want to do this?
In my understanding, CDS is more meaningful, since differential expression at the CDS level indicates potentially different protein outputs...Is this acceptable? Does this behavior have big flaws?
Are you talking about measuring alternate splicing? What exactly are you trying to measure?
What I am going to measure is the gene's expression values (which I hope correspond to protein levels).
The untranslated regions are part of the same mRNA molecule as the CDS. Why would you want to ignore them? You would just be throwing away information about the mRNA abundance.
I am just curious and want to understand the problem which I think is hard to understand. If the unstranslated regions are not useful for the gene's expression values (which I hope correspond to protein levels), I don't think there is a problem to throw them away. On the other hand, if not throwing them away, they may have some negative influence on the exact measurement of gene's expression values (which I hope correspond to protein levels).