Hi Alejandro,

I was reading the messages between you and Fong for testing differential
intron usage.  I am interested in finding intron retention events in my
data as well, since intron retention is the most frequent splicing event in
plants rather than exon skipping. I have already did DEXSeq for
differential exon usage. I was wondering if in preprocessing step, I should
count the reads falling into introns using "dexseq_count.py" and
"dexseq_prepare_annotation.py"? GTF files usually does not have information
about Introns, should I add this information manually? Another question is
that should I count reads falling into exons as well as introns to get
intron retention events? Thanks

	[[alternative HTML version deleted]]

