Aggregating multiple 10 X samples count matrices into one before analysis.

Question

[chanukyapavan4287]

Hi,

I tried to create a common count file for all the samples I have, so I can use it for scRNA seq analysis in R, since I have many samples creating object for each sample and then integrating them would be very time consuming. Currently cell aggr from cellranger will only do for 2 samples, although the 10X cloud allows for multiple files to be aggregated, I don't know whether it will not have accurate data. Also how to generate a cloupe file for all samples combined?

Thanks

[rpolicastro]

The point of integration is to reduce the effect of batch on driving the manifold and clustering. Before you forgo integration you need to QC each sample to check for sample quality and potential batch effect.

[jv]

According to the documentation, cellranger aggr can process more than two samples at a time. You need to include a row in the aggregation csv file for each sample you want to aggregate. Else, if you are getting an error when trying to aggregate more than two samples please share here so we can help troubleshoot. Otherwise, if 10x cloud supports multi-sample aggregation why not use that?

I don't know whether it will not have accurate data.

It is very unclear what you mean by this.

Also how to generate a cloupe file for all samples combined?

Again, according to documentation it looks like cellranger aggr will produce a Loupe file