calculate mappability score for each window

Question

[fatima.m.zare]

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?

[Devon Ryan]

Which genome? You can download mappability tracks from UCSC for some species.

[fatima.m.zare]

I am using human genome (hg19). can I generate by myself instead of using USCS?

Answer 1

[mehran.karimzade]

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.