To study gene expression and splice junctions, we employed two new strategies, designated as RPGM and RPJM. From RNA-seq mapping, we discovered numerous mapped reads at known intron regions, and deep splice junction searches using a gene specific library also identified many novel splice junctions at known intronic and intergenic regions. Previously, RPKM has been used to study gene expression although it is calculated based only on exon models excluding intron and intergenic regions (29). To allow a higher resolution of gene specific splicing, we included sequence information from intronic and intergenic regions and modified the standard RPKM to consider these regions thus defining a new strategy referred to as RPGM. While RPKM is only used for calculations of full-length transcript expression levels, RPGM can be used from the gene level to small regions, such as exons and introns. If gene lengths are larger than the RefSeq Genes model (as observed for GABAB1), RPGM can be calculated based on the new gene lengths. We further considered splice junctions in exon, intron, and intergenic regions and defined a calculation referred to
