DE analysis in nascent RNA Seq based on intron sequences

Question

[MolGeek]

Hi Everyone,

I have nascent RNA-Seq (not spiked) data for multiple conditions and I want to perfom differential expression analysis in the intronic regions to capture nascent differences. After Qc and trimming, I used the STAR for alignment and HTSeq for counting in intronic regions.

I have 2 questions:

1. I am wandering if the default DESeq2 normalization method (median-of-ratios) is suitable for introns, as it assumes that gene expression is on average constant.

2. Is the respective pipeline suitable for intron DE?

Thank you in advance!