The top panel of Supplementary Fig. 2 gives an overview of the RNA-seq data processing pipeline and QC metrics. In detail, reads were mapped to human reference genome hg19 using TopHat version 2.0.9 and Bowtie version 2.1.0, with the following parameters: 0 mismatches in a 20 bp seed, reference guided against Ensembl genes and isoforms (version 70). For each sample, this produced a coordinate-sorted BAM file of mapped paired end reads including those spanning splice junctions, as well as a BAM file of unmapped reads.
