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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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How to integrated the scRNA or scATAC and multiomics data? #5290

Closed Dragonlongzhilin closed 2 years ago

Dragonlongzhilin commented 2 years ago

Seurat and Signac are nice tool to analysis single cell dataset. Recently, I encountered a problem regarding the integration of multiple types of data. I have serveral sample involving scRNA, scATAC and multi-omics(snRNA+snATAC) detected by 10X genomics, and want to integrate them to analysis. But I am confused about how to integrate these data reasonably.

My envisioned plan is as follows: With multi-omics as the center, RNA and ATAC are respectively integrated in sequence (scRNA+snRNA; scATAC+snATAC), and then the wnn method is used to integrate RNA and ATAC. Is this plan feasible?

torkencz commented 2 years ago

Hi, The best course of action should be what you've suggested. Integration across multi omics experiments on RNA-RNA and ATAC-ATAC then the RNA-ATAC integration. As a personal experience RNA-RNA tends to be a little more reliable so I would trust that more.

Dragonlongzhilin commented 2 years ago

Thanks for your reply!

RosaDeSa commented 1 year ago

Hi @Dragonlongzhilin, I am facing a similar challenge. Have you solved it, then?