Estimation of gene expression (RPKM) values was performed as follows:

1. Count the number of reads which map to constitutive exon bodies.  The set of constitutive exons was derived from Ensembl genes (hg18, UCSC genome browser), where an exon was defined to be constitutive if present in all transcripts for a given gene.
2. Determine the number of uniquely mappable positions in the same set of constitutive exons.  "Uniquely mappable" was defined as being a unique 32-mer in the genome and our junction database.
3. Count the total number of uniquely mapping reads in each tissue or sample.
4. Compute RPKM as the number of reads which map per kilobase of exon model per million mapped reads for each gene, for each tissue or sample.