bam2bedgraph: Function converts bam file to bedgraph by counting number of...

In RNAprobR: An R package for analysis of massive parallel sequencing based RNA structure probing data

Description

Function converts bam file to bedgraph by counting number of reads starting at each position (termination counts). It creates two-track bedgraph file (one track for each strand).

Usage

bam2bedgraph(bam_path, allowed_flags = 0:4095, maxMemory = 8000,
  genome_build, bedgraph_out_file = "out_file", track_name = "Track_name",
  track_description = "Track_description")

Arguments

bam_path	path to a bam file to be converted
allowed_flags	integer vector with SAM flags should be kept, see https://broadinstitute.github.io/picard/explain-flags.html for explanation
maxMemory	maxMemory of scanBam function used internally
genome_build	character specifying which UCSC genome build should data be displayed in, e.g. "mm9"
bedgraph_out_file	character specifying prefix of output file. Generated file name is: prefix.bedgraph; if file with such a name already exists new tracks will be appended.
track_name	character specifying track name
track_description	character specifying track description

Value

NULL. Creates a two-track bedgraph file (one track for each strand).

Author(s)

Lukasz Jan Kielpinski

RNAprobR documentation built on Nov. 8, 2020, 5:57 p.m.