issue with merging single cell data files

Question

[Sara]

I have 6 scRNAseq samples from 2 conditions including 3 treatments and 3 controls (from the same run and same experiment) and we have used 10X genomics. I have the samples in separate files in h5 format and trying to find a way to merge them all in a single file but so far did not find a way to do it correctly. my final goal is to perform gene expression analysis and marker detection.

[bompipi95]

In R, you can load in the files individually into Seurat with the Read10x_h5 function into a list, and then merge them all with the merge function there.