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Quality control

AB Abha S. Bais
DC Débora M. Cerqueira
AC Andrew Clugston
AB Andrew J. Bodnar
JH Jacqueline Ho
DK Dennis Kostka
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The Bioconductor102 R package DropletUtils103,104 was used to detect and remove empty droplets with default parameters at an FDR of 0.01, yielding a total of 5,887 non-empty droplets. Multiple quality control (QC) metrics were calculated using the R package scater105 and cells with at least 1000 detected features, and percentage of mitochondrial counts less than 3 times the median absolute deviation (MAD) from the median value were considered, resulting in a total of 4,402 cells. We excluded putative doublets as the top 5% cells ranked by the hybrid score from the R package scds106, further filtering out 220 droplets. Finally, only genes with at least three or more counts in at least three samples were considered, yielding a digital gene expression matrix comprising 11,155 genes in 4,183 cells/droplets.

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