Overall quality control metrics were calculated using RNA-SeQC66 for each sample, including total number of reads (counting twice each fragment sequenced, once for each end in pair), number of mapped reads (again, separately counting each end of a paired end since one may map and not the other), the rates of reads mapping to rRNA, intergenic regions, intragenic regions, introns, exons, and the number of genes and transcripts detected (defined here simply as those with at least 5 exon-mapping reads). UCSC Genome Browser transcripts were used for this quality control (QC) analysis.
