bamQC: Mapping quality control

Description Usage Arguments Value Author(s) Examples

View source: R/bamQC.R

Description

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

Usage

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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

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

ATACseqQC documentation built on Nov. 8, 2020, 11 p.m.