Question: Inclusion of non-coding portions of transcripts (UTR-regions and introns) within the DEX-seq dataset
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3.2 years ago by
ste.depo0 wrote:


I would like to estimate the differential usage of non-coding portions of the transcripts in RNA-seq experiments between two conditions that were derived with non-polyA depletion of rRNAs (e.g. RiboZero), which therefore maintain introinc reads. Moreover, I am interested in the differential usage of the UTRs (5' and 3'). 

My question is: should I include the counts from different portions of the transcripts (coding+non-coding) and analyze the whole information aggregated or should I analyze separately coding and non coding regions (which have different, intrinsic, characteristics, such as increased feature length compared to exons)?



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