ATACseq + scRNAseq merge vignette needed

[davisidarta]

Hi there!

I'm eager to use liger in my analysis. However, I've noticed that there isn't a vignette for using it in order to merge scATACseq and scRNAseq data. Is there any vignette planned, or any further instructions regarding functions to call and the general workflow?

[jw156605]

As a matter of fact, we are about to post just such a vignette! Stay tuned. In the meantime, if you send me an email I can give you some more details. On Jul 22, 2019, at 9:25 PM, davisidarta <notifications@github.com<mailto:notifications@github.com>> wrote: Hi there! I'm eager to use liger in my analysis. However, I've noticed that there isn't a vignette for using it in order to merge scATACseq and scRNAseq data. Is there any vignette planned, or any further instructions regarding functions to call and the general workflow? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#91>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AAS2HVLTGXDBTPW7N6NDS5TQAYCT7ANCNFSM4IF32UCQ>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[davisidarta]

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

Cheers!

[kvshams]

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

Thanks!.

[ccruizm]

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!

[jw156605]

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

[jw156605]

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