I am trying to merge 3 datsets in seurat. I use the vignette on the seura website to merge 2 datasets however when I merge the 3rd t seems like the metadata isnt saved, however the head and tail of the data seem that its all being merged.
It's been a little while since I worked with a 10X dataset (I think they have a newer version of Seurat and cellranger).
However, when I needed to look at more than 2 datasets, I used the aggr function from cellranger.
Please note that you need to add
--normalize=none to get counts similar to the separate quantifications (at least with the version of cellranger that I used).
So, I think the command should look something like this:
/path/to/cellranger-2.1.1/cellranger aggr --normalize=none --id=$AGGR_NAME --csv=$SAMPLE_FILE --localcores=12 --localmem=48
Again, I apologize if this is not exactly the right solution in the latest version of cellranger (or if Seurat has added functionality to accomplish this equally well).