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

ADD COMMENTlinkeditmoderate 10 months ago DrAcula • 0 • updated 10 months ago Charles Warden 6.8k
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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?

ADD REPLYlinkeditmoderate 10 months ago
Friederike
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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).

ADD COMMENTlinkeditmoderate 10 months ago Charles Warden 6.8k

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