Most of my work has been on NGS QC, but lately I've been getting approached with queries for downstream analysis. An investigator was interested in evaluating differential expression of a small set of genes. I ran the investigator's RNASeq datasets through the Tuxedo suite and also through a BWA -> DESeq pipeline to get familiar with established techniques.
Now the investigator wants to focus on expression of a particular murine gene, but only on transcripts which are missing two specific exons. I have the consensus sequences of these exons.
What I'm not sure about is the general strategy to obtain this particular expression information. Having some sort of idea about which tools to investigate would be especially helpful.