Thirty-five- or 75-nucleotide (nt)-long reads were mapped both on to the reference human genome (hg19) and the predicted spliced amplicons with Bowtie 0.12.5 (Langmead et al. 2009). Only uniquely mapping reads with no mismatch were considered to validate a splice site (transcript). Splice junctions were validated if a minimum of 10 reads with the following characteristics spanned the predicted splice junctions. For 35- and 75-nt-long reads, we required at least 4 and 8 nt on each side of the breakpoints (i.e., on each targeted exon), respectively.
