undesirable behavior reading in aggregated 10X data

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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undesirable behavior reading in aggregated 10X data #19

Closed ONeillMB1 closed 4 years ago

ONeillMB1 commented 4 years ago

Neat program you've developed here!

I would like to work form my downsampled data generated with cellranger aggr across several libraries. However, when I used the load10X() function everything is imported as one "Channel". The info is preserved in the barcode endings "-1"...."-10", but the cells are not being imported based on their respective channel/library.

constantAmateur commented 4 years ago

Loading aggregated information in this way is not supported by the load10X function. You can manually construct the channels yourself using the SoupChannel function if you wish, or run SoupX on the un-aggregated data.