blacklist_hg19: Blacklisted genomic regions

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

Description

A GRanges object containing blacklisted regions identified by the ENCODE and modENCODE consortia. These correspond to artifact regions that tend to show artificially high signal (excessive unstructured anomalous reads mapping). Selected from mappability track of the UCSC genome browser (hg19, wgEncodeDacMapabilityConsensusExcludable and wgEncodeDukeMapabilityRegionsExcludable tables).

Code used to retrieve these regions:

• curl http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed > hg19_DACExcludable.txt
  

• cat hg19_DUKEExcludable.txt hg19_DACExcludable.txt | grep -v "^#" | cut -f 2,3,4,5,6,7 | sort -k1,1 -k2,2n | mergeBed -nms -i stdin > hg19_DUKE_DAC.bed
  

Used as 'RegionsToFilter' within the QCfilter function so that variants overlapping these regions will be removed.

Format

A GRanges object of 1378 ranges.

Details

Note that these blacklists are applicable to functional genomic data (e.g. ChIP-seq, MNase-seq, DNase-seq, FAIRE-seq) of short reads (20-100bp reads). These are not applicable to RNA-seq or other transcriptome data types.

Author(s)

Ines de Santiago [e-mail]

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