Phase specific expression using DeSeq2 or edgeR

Question

[vskale135]

Hello All, we have haplotype resolved assembly for a crop plant. By comparing the phases, we have identified 24K paired genes between phases. We have collected RNASeq data for different seed development stages( s1,s2, s3, and s4) and would like to study phase specific expression within and between stages. As the genes were highly diverged, the RNASeq reads were mapped to 48K transcripts. I would like to know how to model this if I want to use DeSeq2 or edgeR package? Thanks and regards

[ATpoint]

You might be interested in the seesaw sectionmof fishpond: https://bioconductor.org/packages/release/bioc/html/fishpond.html

[vskale135]

Thanks Alot for reply. I have gone through the package you mentioned. The package is for allele specific expression which uses VCF file to generate dummy diploid genome. In my case, we have diploid genome and I would like to study expression difference between gene pairs. I found this post https://support.bioconductor.org/p/75182/ but not completely sure how to generate design matrix.

With best regards

Sandip