Normalization of single cell allele counts RNA-seq analysis

Question

[luckysardar171]

Hi guys,

I 'm working on single cell allelic counts RNAseq data with the heterogenous cell population and I have the allelic raw read read count files for example AlleleA and AlleleB, my objective is to do genome wide analysis, for downstream I have to normalize the data. I am thinking of trying Deseq2, edgeR TMM normalization, but I am confused is it okay to use or not. any one suggest me with this type analysis how I have to proceed, I went through various threads I did'nt find any clear answer. or I can proceed without normalization will be better please suggest me

Method to get normalize allele specific read counts

Thank you