processCUTTAG: Automated processing of CUT&TAG samples
In mireia-bioinfo/pipelineNGS: Methods for Epigenetic Data Processing

processCUTTAG

R Documentation

Automated processing of CUT&TAG samples

Description

DEPRECATED! Use process_epigenome() with seq_type="CT" instead.

Usage

processCUTTAG(
  fastq_files,
  out_name,
  type = "PE",
  run_fastqc = TRUE,
  path_fastqc = "FastQC/",
  path_bam = "BAM/",
  path_peaks = "Peaks/",
  path_logs = "Logs/",
  index = "/biodata/indices/species/Hsapiens/ucsc.hg19",
  remove = c("chrM", "chrUn", "_random", "_hap", "_gl", "EBV"),
  blacklist = "~/data/consensusBlacklist.bed",
  gen_sizes = "",
  seacr_type = "stingent",
  seacr_top = 0.01,
  cores = 8,
  bedtools_bamtobed = "bedtools bamtobed",
  bedtools_genomecov = "bedtools genomecov",
  seacr = "SEACR_1.3.sh"
)

Arguments

`fastq_files`	List containing the different FastQ file pairs (one list element for each sample).
`out_name`	Sample name to use for each of the samples.
`type`	Character indicating if reads are paired end (PE) or single end (SE).
`run_fastqc`	Logical indicating whether to run FastQC or not.
`path_fastqc`	Path for the FastQC results.
`path_bam`	Path for the aligment and filtering results.
`path_peaks`	Path for the peak files.
`path_logs`	Path for the logs.
`index`	Path to the index needed by Bowtie2.
`remove`	List of chromosomes to remove from final BAM file.
`blacklist`	List of blaclisted regions to remove from BAM file.
`gen_sizes`	Chromosome sizes to use for bedgraph conversion.
`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.
`cores`	Number of threads to use for the analysis.
`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.