EU-Seq Differentially expressed transcripts

Question

[Bruno]

Hi everyone. I'm wondering if any one can help me to stablish a correct way to find differentially expressed transcripts from nascent RNA Seq data (EU-Seq). I have found plenty documentation for GRO-Seq and csRNAseq, but barely any info on EU-Seq.

In a paper describing methods for the technique (https://www.sciencedirect.com/science/article/pii/S2666166721003580?via%3Dihub) they show how to subtract the noEU effect from the other samples. The problem now is you obtain a normalized count matrix and you can't input that to DESeq2. How can I subtract the noEU effect, and also find differentially expressed transcripts?

Any help is highly appriciated.

Thanks in advance.