allCells extension plate

[ii-bioinfo-thomas]

Hi,

if you use the individual allCells files of each plate (as I've understood from doc), you're missing cells in "cellMetrics.filtered.csv". I assume the reason is that scaleRNA is re-filtering the cells upon merging the plates resulting in a different cell list then the concatenation of the individual plates. Is it correct to split the *.merged.allCells.csv into files corresponding to the plates RNA-A-AP[1-4] or can I use the merged.allCells file? If splitting is required, do I've to remove the suffix indicating the plate from each barcode in the allCells file?

Thanks,
Thomas