Question: DEXSeq : for differential exon usage
gravatar for gv
14 months ago by
United States
gv30 wrote:


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.





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