I want to remove mappability bias from my data (bam file) and so I should calculate mappability score first. Actually I want to have windows with size 100bp. Is there any way to calculate mappability score for each window?
You can use per-base mappability tracks of hg19 for several common short-read sequencing read lengths (24, 36, 50, and 100) from http://bismap.hoffmanlab.org/. You can download the files in wiggle or BED.