Hello,
I'm interested in finding expression of known imprinted genes (expressed from one allele only, monoallelic expression) within each cluster in my single-cell RNA-sequencing (scRNA-seq) data generated from 3' transcript using 10x genomics. I also wanted to identify novel expressed imprinted genes within each cluster from this data. This scRNA-seq data comes from offspring tissues generated by crossing two different parent mouse strains with known genomic single nucleotide variants/ polymorphisms (SNPs/SNVs). What is the best approach for conducting this analysis? Is there any pipeline available for this purpose?
Thank you