Question: Detecting differential usage of introns from RNA-seq data.
6.5 years ago by
Delasa Aghamirzaie • 70
Delasa Aghamirzaie • 70 wrote:
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]]
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