bamToBigWig: Conversion from BAM to visualization formats

In mireia-bioinfo/pipelineNGS: Methods for Epigenetic Data Processing

Conversion from BAM to visualization formats

Description

Converts post-processed BAM files to visualization formats such as BedGraph (compressed) and BigWig.

Usage

bamToBigWig(
  bamfile,
  scaling_factor = 1,
  path_bw,
  chr_sizes,
  bedtools_genomecov = "bedtools genomecov",
  bdg_to_bw = "bedGraphToBigWig",
  uncompressed_bw = FALSE,
  cores = 5,
  perc_mem = "50%"
)

Arguments

bamfile	Path and name of the bam file to convert.
scaling_factor	Factor to use for scaling.
path_bw	Character string indicating the path where you want to save visualization files (it will be created if it does not exist).
chr_sizes	Character string indicating the path where the file with chromosome name and sizes can be found.
bedtools_genomecov	Character string indicating the path where the program converter from bedGraph to BigWig can be found. Default assumes it is in your PATH.
bdg_to_bw	Character string indicating the path where the bedtools genomecov binary can be found. Default assumes it is in your PATH.
uncompressed_bw	Logical indicating whether to compress or not the resulting bigWig file.
cores	Number of cores to use.
perc_mem	Percentage of memory to use.

Value

Two visualization files: bedgraph (.bdg) and bigwig (.bw) in your path_bw.

mireia-bioinfo/pipelineNGS documentation built on Jan. 2, 2023, 11:18 a.m.