Question: Detecting differential usage of introns from RNA-seq data.
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gravatar for Delasa Aghamirzaie
6.5 years ago by
United States
Delasa Aghamirzaie70 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]]
preprocessing dexseq • 1.5k views
ADD COMMENTlink modified 6.5 years ago by Alejandro Reyes1.7k • written 6.5 years ago by Delasa Aghamirzaie70
Answer: Detecting differential usage of introns from RNA-seq data.
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gravatar for Alejandro Reyes
6.5 years ago by
Alejandro Reyes1.7k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.7k wrote:
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
ADD COMMENTlink written 6.5 years ago by Alejandro Reyes1.7k
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