Multiome Dataset
Sayyam-Shah opened this issue · 4 comments
Hello,
I hope you are doing well. Thank you for the amazing tool.
I have a multiome dataset on the same cells and would like to take advantage of SEAcells. Would you recommend I run the seacell algorithm on both modalities separately and map the ATAC seacells to the RNA seacells?
We recommend using the ATAC metacells for the use of gene-peak associations, gene scores and other ATAC related computation.
Interesting, thank you!
Why do you recommend using the ATAC metacells to compute the RNA summarized seacells? I am hoping to run Scenic+ on my data. It uses the ATAC and RNA data to identify TFs.
You can also try using the SCENIC+ latent representation to compute metacells instead of SVD.
That's an amazing idea. I assume you are referring to the reduction method used to generate the UMAP with pycistopic.
From there, I can compute the ATAC and RNA seacells using the latent representation from cistopic on the full dataset. Then I can run cistopic again on the seacells and run scenic+ with the RNA seacells.