I'm working with a mutant that is supposed to show gene-specific splicing defect (1), readthrough (2) and spurious transcription (3). From paired-end strand-specific RNA-seq data, what would you do to identify the affected loci ? How would you communicate (in terms of figures) the results ?
I was thinking running DESeq on introns (1) and 5'/3' flanking sequences (2) while keeping the normalization on the exon read count. Or maybe just use the ratio
(reads mapping on intron)/(reads mapping on exons) What do you think of this approach ?
I'd really appreciate any input on this ! Thanks in advance !