In rujinwang/WGSmapp: Mappability tracks of Whole-genome Sequencing from the ENCODE Project

Mappability

This package provides whole-genome mappability tracks on human hg19/hg38 assembly. We employed the 100-mers mappability track from the ENCODE Project and computed weighted average of the mappability scores if multiple ENCODE regions overlap with the same bin.

library(WGSmapp)
data("mapp_hg19")
mapp_hg19

Blacklist regions

hg19

For hg19 reference genome, “blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are included.

library(WGSmapp)
# Get segmental duplication regions
seg.dup = read.table(system.file("extdata", "GRCh37GenomicSuperDup.tab", package = "WGSmapp"), head = TRUE)
# Get hg19 gaps
gaps = read.table(system.file("extdata", "hg19gaps.txt", package = "WGSmapp"), head = TRUE)

head(seg.dup)
head(gaps)

hg38

For hg38 reference genome, “blacklist” bins, including segmental duplication regions and gaps in reference assembly from telomere, centromere, and/or heterochromatin regions are also incorporated in the package.

library(WGSmapp)
# Get segmental duplication regions
seg.dup.hg38 = read.table(system.file("extdata", "GRCh38GenomicSuperDup.tab", package = "WGSmapp"))
# Get hg38 gaps
gaps.hg38 = read.table(system.file("extdata", "hg38gaps.txt", package = "WGSmapp"))

head(seg.dup.hg38)
head(gaps.hg38)

BAM files

The dataset consists of three assembled .bam files of single-cell whole genome sequencing from 10X Genomics Single-Cell CNV solution for illustration purposes. These three cells are from section E of five adjacent tumor dissections of a breast cancer patient. Corresponding cellular barcode tags are "AAAGCAATCTGACGCG", "GCAGTTACACTGTATG", and "CTCGTCACAGGTTAAA".

rujinwang/WGSmapp documentation built on April 6, 2020, 12:10 p.m.