ATACseq + scRNAseq merge vignette needed about liger HOT 6 CLOSED

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Thank you for the ultra fast answer, @jw156605 ! I emailed you accordingly.

Cheers!

from liger.

@jw156605 Is that vignette available now? Will that have functions to merge cross species data?

Thanks!.

from liger.

Hello @jw156605,

I would also like to try your tool for my analysis and would need the vignette as a guide to integrate scATAC and scRNA data.

Thanks in advance!

from liger.

I'm just about to post the vignette, but the punchline is that running Liger with default settings on RNA and ATAC works quite well. To construct the ATAC matrix, just sum promoter and gene body peaks or raw counts (raw counts preferred, since the 10X peak calling is biased against rare cell populations) for each gene. We have written a fast Rcpp function that takes the 10X filtered fragment file and produces gene counts, or you can use the output from the Seurat function that sums peaks. Then perform gene selection on the RNA data only and use these genes for joint factorization just as in the RNA vignette. Alternatively, you can load your RNA and ATAC data into a Seurat object, then use Seurat wrappers to run Liger on it: https://htmlpreview.github.io/?https://github.com/satijalab/seurat.wrappers/blob/master/docs/liger.html

from liger.

A vignette showing how to integrate RNA and ATAC data is now available at: https://macoskolab.github.io/liger/walkthrough_rna_atac.html

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