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]]

Dear Delasa Aghamirzaie, I did this once and it worked fine. Just make sure you have strand specific data or to have a close look at your hits (you might confound your hits with any kind of antisense transcripts differentially expressed). The DEXSeq python scripts should do the job (also allowing counting those reads that fall partially in an exon or an intron), you just need to add to the "flattened annotation file" the information about your introns. Best regards, Alejandro > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor