process_epigenome: Automated processing of ChIP-seq and ATAC-seq samples

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

Automated processing of ChIP-seq and ATAC-seq samples

Description

This function performs all necessary steps in the ChIP-seq processing pipeline.

Usage

process_epigenome(
  fastq_files,
  out_name = NULL,
  seq_type = c("ATAC", "CHIP", "CT"),
  type = "SE",
  cores = 8,
  path_fastqc = "FastQC/",
  path_bam = "BAM/",
  path_peaks = "Peaks/",
  path_logs = "Logs/",
  run_fastqc = TRUE,
  index = "/vault/refs/indexes/hg38",
  extra_bowtie2 = "",
  remove = c("chrM", "chrUn", "_random", "_hap", "_gl", "EBVls"),
  blacklist = "/vault/refs/hg38-blacklist.v2.bed",
  type_peak = c("narrow", "broad"),
  shift = c(TRUE, FALSE),
  chunk = 1e+07,
  gen_sizes = "/vault/refs/hg38.chromSizes.txt"
)

Arguments

fastq_files	Character string (single-end) or character vector of length 2 (paired-end) with the file names of the samples to be analysed.
out_name	Character vector, with the same length as fastq_files, indicating the output filenames.
seq_type	Experiment type, either "ATAC" (default) or "CHIP".
type	Sequence type, one of "SE" (single end) or "PE" (paired end).
cores	Number of threads to use for the analysis.
path_fastqc	Character indicating the output directory for the FastQC reports.
path_bam	Character indicating the output directory for the bam files.
path_peaks	Character indicating the output directory for the peak files.
path_logs	Character indicating the output directory for the logs.
run_fastqc	Logical indcating whether to run (TRUE) or not (FALSE) FastQC. Default: TRUE.
index	Character indicating the location and basename for the Bowtie2 index.
extra_bowtie2	Character containing additional arguments to be passed to bowtie2 alignment call.
remove	Character vector with chr that will be filtered out. Any chromosome name containing matches for these characters will be removed.
blacklist	Character indicating the file containing blacklist regions in bed format. Any reads overlapping these regions will be discarded.
type_peak	Character indicating the type of peak to be called with MACS2, either "narrow" or "broad".
shift	Logical indicating whether the reads should be shifted -100bp and extended to 200bp (TRUE) or not (FALSE, default).
chunk	Size of the chunk to load into memory for ATAC-seq read offset. This argument is necessary only when type="SE".
gen_sizes	Character string indicating the path where the file with chromosome name and sizes can be found. This argument is necessary only when type="SE".

Details

This function ocesses ATAC-seq or ChIP-seq from FastQ files using the following pipeline:

1. Quality Control (FastQC).

2. Alignment to reference genome (Bowtie2).

3. Post-processing (Samtools), including removing duplicates, blacklisted regions and non-reference chromosomes.

4. (only for ATAC-seq) Offset correction (Samtools).

5. Peak calling (MACS2).

This function can process paired and single end FastQ files:

• Single end files. The argument fastq_files should be a character vector with the name of each file.

• Paired end files. The argument fastq_files should be a list, where each element is a vector of size 1, where the first one is the R1 and the second one is the R2.

Value

Creates the folders path_fastqc, path_bam, path_peaks, path_logs, by default in your working directory, containing the output files from de different analyses.

Examples

## Not run: 
process_epigenome(fastq_files=c("path/to/file.fastq.gz", "path/to/file2.fastq.gz"),
                  seq_type="ATAC",
                  out_name=c("sample1", "sample2"),
                  type="SE",
                  cores=8)

## End(Not run)

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