Dear all,
We performed a scRNA-seq experiment using the cell hashing protocol devolped by the Satija lab. This allows us to 'overload' the 10X Chip Channel, knowing that we will be able to detect most doublets in our dataset as those cell barcodes that express more than one hashtag. As a control for each sample, we added non-hashed cells to another well in the same 10X Chip, to later assess if this protocol is introducing any artifacts. To perform this comparison, I would like to merge both expression matrices (coming from different cellranger count) into a single one using cellranger aggr, as described here. This is of special importance as this two GEM wells have markedly different sequencing depths. However, I'm not entirely sure whether this will impact the demultiplexing of the hashtags in subsequent steps.
So, my question is: should I run cellranger aggr? If not, how could I correct for these differences?
Thanks a lot in advance,
R