How can you merge more than two 10x datasets in Seurat?

Question

[DrAcula]

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.

[Friederike]

when I merge the 3rd t seems like the metadata isnt saved

I'm not sure I completely understand what's going on -- could you perhaps post the results of str() on the individual files as well as the merged files and keep the commands you run in between as well?

Answer 1

[Charles Warden]

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).