UniqueMappability50bp_hg19: Genomic regions of unique mappability

In BaalChIP: BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Description

A GRanges object containing unique regions with genomic mappability score equal to 1. Selected from DUKE uniqueness mappability track of the UCSC genome browser (hg19, wgEncodeCrgMapabilityAlign50mer table).

Code used to retrieve these regions:

• curl http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeCrgMapabilityAlign50mer.bw > wgEncodeCrgMapabilityAlign50mer.bw

• ./bigWigToBedGraph wgEncodeCrgMapabilityAlign50mer.bw wgEncodeCrgMapabilityAlign50mer.bedgraph

• awk ' if ($4 >= 1) print $0 ' wgEncodeCrgMapabilityAlign50mer.bedgraph > wgEncodeCrgMapabilityAlign50mer_UNIQUEregions.bedgraph

Used as 'RegionsToKeep' within the QCfilter function so that variants NOT overlapping these regions will be removed.

Format

A GRanges object of 9831690 ranges.

Details

These regions are not applicable to longer reads (> 50bp).

Author(s)

Ines de Santiago [e-mail]

Source

Downloaded from http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeCrgMapabilityAlign50mer.bw.

BaalChIP documentation built on Nov. 8, 2020, 5:23 p.m.