makeCutCountBAMWithName: Make a cutcount data file from a BAM file

In sojbaek/bagfootr: Bi-vAriate Genomic Footprinting (BaGFoot)

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

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.