makeCutCountBAMWithName: Make a cutcount data file from a BAM file

Description Usage Arguments Value

View source: R/bfoot.R

Description

This function reads a bam file and convert it to a BedGraph file which contains counts of cuts (DNase) or insertions on the genomic locations.

Usage

1
makeCutCountBAMWithName(bamFile, name = "", refgenome = "mm9", atac = F)

Arguments

name

Name of the output bedgraph file

refgenome

Reference genome, eg) "mm9", "hg19"

atac

Logical TRUE for ATAC-seq

bamfile

Path to the input bam file

Value

Bedgraph filename


sojbaek/bagfootr documentation built on Aug. 22, 2020, 9:44 p.m.