Integration of different multiome library

[adrdufour]

Hello,

I would like to know the best way to integrate multiple 10x multiome (scRNAseq + scATACseq) analyses together. I noticed that RNAseq have much more difficulties to be integrated together as you can see in the joined images.

Thanks for your responses.

[rcorces]

I'm afraid I dont have specific suggestions for this. You can, of course, tweak the harmony parameters to try to get a better batch correction. But why not just use the LSI_ATAC for your dimensionality reduction and proceed with that? There is nothing that says you have to use a combined dim reduction or use any info on the RNA side for this.