Calculating mapability is really straightforward: Take a reference genome's fasta file and generate all possible reads of a given length. Map those reads back to the reference genome, and identify which of them map uniquely in the expected location. You'll find some very simple bash/perl code that wraps BWA and then calculates mapability and gc-content scores in 100bp windows here: https://code.google.com/p... Keep in mind that this code only generates single-end reads, but by using paired-end reads, you up your mapability significantly. The code could easily be tweaked to do that. Be sure to think about what insert size is appropriate. There are also some precomputed mappability tracks available for download through the UCSC table browser. - Chris Miller