peakCallingSEACR: CUT&TAG peak calling with SEACR

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

CUT&TAG peak calling with SEACR

Description

CUT&TAG peak calling with SEACR

Usage

peakCallingSEACR(
  bam_file,
  path_peaks,
  gen_sizes,
  cores = 5,
  seacr_type = "stingent",
  seacr_top = 0.01,
  bedtools_bamtobed = "bedtools bamtobed",
  bedtools_genomecov = "bedtools genomecov",
  seacr = "SEACR_1.3.sh"
)

Arguments

path_peaks	Path for the peak files.
gen_sizes	Chromosome sizes to use for bedgraph conversion.
cores	Number of threads to use for the analysis.
seacr_type	Type of peaks to call with SEACR, either "stringent" (default) or "relaxed."
seacr_top	A numeric threshold n between 0 and 1 returns the top n fraction of peaks based on total signal within peaks. Default: 0.01.
bedtools_bamtobed	Path or alias of the bedtools bamtobed utility.
bedtools_genomecov	Path or alias of the bedtools genomecov utility.
seacr	Path or alias of the SEACR utilty.

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