FastQC was applied to DIAN and Knight-ADRC RNA-seq data to perform quality checks on various aspects of sequencing quality [47]. The DIAN and Knight-ADRC dataset was aligned to human GRCh37 primary assembly using Star (ver 2.5.2b) [48]. We used the primary assembly and aligned reads to the assembled chromosomes, un-localized and unplaced scaffolds, and discarded alternative haploid sequences. Sequencing metrics, including coverage, distribution of reads in the genome [49], ribosomal and mitochondrial contents, and alignment quality, were further obtained by applying Picard CollectRnaSeqMetrics (ver 2.8.2) to detect sample deviation. Additional QC metrics can be found in Additional file 1: Table S1.
