How to download the low mappability regions from the UCSC browser

Question

[bioinforesearchquestions]

Hi All,

1) What are all low mapability regions? 2) How to download the low mapability regions from the UCSC browser?

Answer 1

[GenoMax]

Mapability and read length are described in this paper.

You can download "mapability" tracks from UCSC Table browser. They seem to be available for hg19 build. Select group "Mapping and Sequencing" and track "Mappability". Multiple options available in terms of k-mers and you can send the data to bed format files.

[bioinforesearchquestions]

Thanks, genomax2.

I have already found SNPs and CNVs. Now I am planning to exclude those SNPs and CNVs which fall under the low mappability region. I have some read length of 101 and 151 bases. Which one do I to select?

"CRG Align 24 (WgEncodeCrgMapabiltyAlign24mer"

"CRG Align 36 (WgEncodeCrgMapabiltyAlign36mer"

"CRG Align 40 (WgEncodeCrgMapabiltyAlign40mer"

"CRG Align 50 (WgEncodeCrgMapabiltyAlign50mer"

"CRG Align 75 (WgEncodeCrgMapabiltyAlign75mer"

"CRG Align 100 (WgEncodeCrgMapabiltyAlign100mer"

"Duke Uniq 20"

"Duke Uniq 35"

"DAC backlist"

"Duke Excluded"