Workflow of allele-specific gene expression analysis in case study 2. (a) 2D scatter plot of CASTEiJ (CAST) vs. C57BL6J (B6) allelic read counts. (b) genes with allelic skew labeled by "1" for CAST and "-1" for B6 skew. (c-d) Pie charts showing chromosomal distribution of CAST vs. B6 specific expressed genes. (e) CAST contribution for H3K36me3 vs. RNA-seq. (f) genome browser view of "Slc38a4" and "Mirg" imprinted genes with mono-allelic expression in B6 and CAST.