Simulating an allele-specific RNA-seq experiment. Reads were generated from the “reference” D. melanogaster (dm3) allele (blue) and from an “alternative” allele (red) that contained all homozygous single nucleotide variants found in the DGRP strain “line_40”. For each exon, one read (arrow) was generated starting at each position for each allele from 1 to n-k, where n is the length of the exon and k is the length of the read, both in bases. This process was repeated for the reverse complement of each exon. The black arrows indicate reads with no allele-specific information.