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Old 04-14-2014, 01:36 PM   #1
xguo
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Location: Maryland

Join Date: Jul 2008
Posts: 48
Default DEXSeq for intron retention

Dear all,
I'm trying to use DEXSeq to detect intron retention events in diseased human samples. Essentially we need to count how many reads map to each intron and then use DEXSeq to do statistical comparison. My question is how we shall prepare the intron annotation and count files for DEXSeq. One way is to retrieve intron gtf file from UCSC table browser, and collapse them into intronic counting bins. The other way is to extract intron coordinates based on exon gtf file prepared by dexseq_prepare_annotation.py included in DEXSeq.

Does anyone have experience in identification of differential intron retention using DEXSeq? It'll be great if you can share your insights in the preparation of intron count files.

thanks
Xiang
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