I am performing an allele-specific RNA-seq analysis. Basically, I used SNP positions between two alleles of a mouse hybrid strain to separate reads specific to each allele. Now I normalized the data, as usual, using Deseq2 function and performed differential expression analysis.
However, I wonder if the normalization method for allele-specific counts will be the same or different from regular RNA-seq. If I consider only sequencing depth normalization (CPM: counts per million), the regular RNA-seq data will be normalized by total mapped reads and multiplied by 1M.
But now since I already separated my reads specific to two different alleles, does the same normalization method will make sense? In this case, instead of the total mapped reads, I used total reads assigned to each allele and normalized following counts per million (CPM) method.
I read a few things in this post about a similar topic but still not clear to me how should I proceed?