Is an RNA modality file from multiome needed/necessary to annotate clusters in scATAC dataset?

kaizhang / SnapATAC2

Single-cell epigenomics analysis tools

https://kzhang.org/SnapATAC2/

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Is an RNA modality file from multiome needed/necessary to annotate clusters in scATAC dataset? #323

Closed yojetsharma closed 1 month ago

yojetsharma commented 2 months ago

The tutorial mentions use of a RNA multiome file[(reference = snap.read(snap.datasets.pbmc10k_multiome(), backed=None)] for annotation of clusters in scATAC dataset (https://kzhang.org/SnapATAC2/tutorials/annotation.html).

kaizhang commented 2 months ago

This is not necessary. You can annotate the cells based on marker genes' activity.

yojetsharma commented 2 months ago

Is there a tutorial for how to do that? I am new to this so still trying to my find my footing. How can I just my scRNA seq to annotate the scATAC clusters?

kaizhang commented 2 months ago

What data do you have, scATAC or single-cell multiome dataset?

yojetsharma commented 2 months ago

I have a single-cell multiome dataset from multiple samples that I want to process as concatenated/merged anndata object.