bam2bedgraph

bam_path

integer vector with SAM flags should be kept, see https://broadinstitute.github.io/picard/explain-flags.html for explanation

allowed_flags

maxMemory of scanBam function used internally

maxMemory

character specifying which UCSC genome build should data
be displayed in, e.g. "mm9"

genome_build

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.

bedgraph_out_file

track_name

track_description

This package facilitates analysis of Next Generation Sequencing
data for which positional information with a single nucleotide resolution
is a key. It allows for applying different types of relevant
normalizations, data visualization and export in a table or UCSC
compatible bedgraph file.

Nikos Sidiropoulos

RNAprobR

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

bam2bedgraph function

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).

bam2bedgraph: 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).

Description

Usage

Arguments