This is a test version of Biostars. For the public version, visit https://www.biostars.org.
calculate mappability score for each window

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
• 3,873 views • link
updated by mehran.karimzade mehran.karimzade • written by fatima.m.zare • fatima.m.zare

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

• 0 views • link
written by Devon Ryan Devon Ryan

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

• 0 views • link
written by fatima.m.zare • fatima.m.zare

1 answer

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.

• 0 views • link
written by mehran.karimzade mehran.karimzade

Log in to answer this question.

More posts like this