I am trying you use DEXSeq package for differential exon usage. I am interested in only a single exon(hence single gene) to see how differently it is used under different conditions. I created the gff file for only that gene having the exon I am interested in.
Is it fine to run DEXSeq for only that particular exon i.e. I get counts for all the exons of that particular gene only? Will it some how effect the normalization step which takes into account coverage biases for different samples?
I am doing this since my samples are huge in terms of number of reads and processing takes a lot of time.
Let me know if this sounds to be a fine way to perform the analysis.