calculate mappability score for each window
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4.4 years ago

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?

mappability score bias mappability bias • 1.9k views
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Which genome? You can download mappability tracks from UCSC for some species.

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

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3.9 years ago

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.

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