Alignment, initial quality control and quantification differed slightly across datasets, as described in the Supplementary Note. Each cohort removed outliers as described above, and then used Trimmed Mean of M-values normalization59 and a counts per million (CPM) filter to include genes with >0.5 CPM in at least 1% of the samples. Subsequent steps were identical to the Illumina processing, with some exceptions for the BIOS Consortium datasets (Supplementary Note).
