bamQC: Mapping quality control

In jianhong/ATACseqQC: ATAC-seq Quality Control

Mapping quality control

Description

Check the mapping rate, PCR duplication rate, and mitochondria reads contamination.

Usage

bamQC(
  bamfile,
  index = bamfile,
  mitochondria = "chrM",
  outPath = sub(".bam", ".clean.bam", basename(bamfile)),
  doubleCheckDup = FALSE
)

Arguments

bamfile	character(1). File name of bam.
index	character(1). File name of index file.
mitochondria	character(1). Sequence name of mitochondria.
outPath	character(1). File name of cleaned bam.
doubleCheckDup	logical(1). Double check duplicates or not if there is no tags for that.

Value

A list of quality summary.

Author(s)

Jianhong Ou

Examples

bamfile <- system.file("extdata", "GL1.bam", package="ATACseqQC")
bamQC(bamfile, outPath=NULL)

jianhong/ATACseqQC documentation built on June 14, 2025, 1:23 a.m.