Question: Inclusion of non-coding portions of transcripts (UTR-regions and introns) within the DEX-seq dataset
0
gravatar for ste.depo
2.9 years ago by
ste.depo0
ste.depo0 wrote:

Hello,

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)?

Thanks,

Stefano 

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by ste.depo0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 247 users visited in the last hour