Normalisation of allele specific read counts from Single cell RNA seq data

[DeepshikhaChandel]

Hello Sir/Ma'am, A very convincing normalisation approach well explained in the paper.

So we have the allele specific read count from Single-cell RNA seq data without any spike-ins Or UMI's. Can we use Quminorm to normalise these allelic reads. If yes, Can you provide us with a detailed methodology or explain us how to apply Quminorm to our single-cell RNA seq allelic data.?

Thank you so much, Deepshikha

[willtownes]

Thanks for your interest! I'm not very familiar with "allelic reads" (could you provide a reference for this?) but you are welcome to give it a try. The R package is installable from https://github.com/willtownes/quminorm .

[DeepshikhaChandel]

@willtownes Thanks for your valuable response. So I haven't come across any paper where people have used Quminorm for Single-cell allelic read count normalisation. As Single-cell RNA seq technology itself is, you can say not very old one, so there are very few studies which have actually performed normalisation on allelic reads using sequencing depth normalisation as DESeq2 or TMM normalisation.

So was just curious to see if your method applies to our needs at the moment, that is, Can Quminorm be used for allelic reads normalisation obtained from single-cell RNA seq data ?

Best, Deepshikha

[willtownes]

I guess the short answer is "I don't know". Feel free to give it a try but I can't promise anything since we didn't test it on that particular type of data.