Automated processing of CUT&TAG samples — processCUTTAG • pipelineNGS

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.