Single-cell RNA seq allelic data normalisation

[DeepshikhaChandel]

Well explained tool for Single-cell RNA seq data normalisation !

Hi,
So we are normalising the Single-cell RNA seq data and we now have to normalise the allelic read counts. Scnorm seems to be quite convincing for Single-cell data. But we are confused if it will work well for our allelic reads as well. Can you please suggest us a detailed protocol for that. It would be really helpful to us.

For our analysis we have datasets from different studies, thus heterogenous single-cell RNA seq data is what we are analysing.

Thanks in advance,
Deepshikha

[rhondabacher]

Hi Deepshikha, I have not yet tested SCnom on allelic read counts, but I don't foresee any problems. I'd be interested to see the results. Best, Rhonda

…

On Wed, Sep 16, 2020 at 6:38 AM DeepshikhaChandel ***@***.***> wrote: Well explained tool for Single-cell RNA seq data normalisation ! Hi, So we are normalising the Single-cell RNA seq data and we now have to normalise the allelic read counts. Scnorm seems to be quite convincing for Single-cell data. But we are confused if it will work well for our allelic reads as well. Can you please suggest us a detailed protocol for that. It would be really helpful to us. For our analysis we have datasets from different studies, thus heterogenous single-cell RNA seq data is what we are analysing. Thanks in advance, Deepshikha — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#31>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABSOD3BTXQZ4RXUFR7E2IHDSGCIRTANCNFSM4ROT2WVA> .

-- Rhonda Bacher, PhD Assistant Professor Department of Biostatistics University of Florida Office: 5239 CTRB Phone: 352-294-5914 Email: rbacher@ufl.edu http://rhondabacher.com/