New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Integration of multiple scATAC samples #251

Open

rLannes opened this issue Jan 12, 2022 · 0 comments

Labels

question

rLannes commented Jan 12, 2022

Hi,
First, thank you for providing the community with such a tool.

I have 10 sc ATAC seq from 10 different tumors. I have corresponding scRNA-seq (same tumor, not multi-omics) for 6 samples.

Question:

As a first step I would like to integrate the scATAC, IS this possible with Liger?
- if so should I do that on peaks? or on features (number of peaks on genes/promoters)?
Secondly, I would like to integrate all my data using your vignette. From what I understand not having the corresponding RNA-seq for some samples may complicate the analyses. Should I remove the sample for which I don't have the corresponding RNA-seq?

Thank you for your help.
Romain

theAeon added the question label

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment