I have RNAseq data of a hybrid yeast, which has a lot of gene conversion and loss of heterozygosity between two genomes. I also have RNAseq data of one of its parents.
I was able to phase only 300 genes out of 6000. What I want is to compare gene expression levels between hybrid and this parent. Since only these 300 genes are phased, I got only 2% of uniquely mapped reads in hybrid, while in parent there are around 90%.
So my question is whether it is legitimate to use DESeq2 for only this subset of 300 genes? I am wondering whether it is ok to compare such a different library sizes together.