The question has three parts: What is different between the RNA-seq and whole exome sequencing? I know the inputs are different in that one uses RNA (mRNA/ total RNA etc), and the other uses DNA. However, I would like to know how the selection/ purification step in whole-exome sequencing is performed? And, in terms of sequencing output, is there any difference between these two technologies?
Is it possible to detect SNP within the coding/ transcribed regions with RNAseq data? Is there any software/ program that has been developed to perform such analysis? Or I should go for the standard programs used for the whole-exome sequencing (if they are the same as mentioned in the first part of the question)?
I am a novice of SNP/ structural variance detection, may I know is there any standard pipeline that can perform such work for both whole-genome sequencing and exome sequencing? I guess I will at least need the variant calling result. It would be nice if you can also suggest some resources or reading for me what will be the usual downstream analysis for this type of data.
Thank you!
