cfDNAWGBS2

This function is used for case/control analysis of paired/single end WGBS data.

Note

User must set pipeConfigure2 before using.

Parameters

cfDNAWGBS2(caseFolder=None,
           ctrlFolder=None,
           caseName=None,
           ctrlName=None,
           caseFq1=None,
           caseFq2=None,
           ctrlFq1=None,
           ctrlFq2=None,
           caseAdapter1=["AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"],
           caseAdapter2=["AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"],
           ctrlAdapter1=["AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"],
           ctrlAdapter2=["AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"],
           fastqcOP=None,
           idAdapter=True,
           idAdOP=None,
           rmAdapter=True,
           rmAdOP={"--qualitybase": 33, "--gzip": True},
           bismarkOP={"-q": True, "--phred33-quals": True, "--bowtie2": True, "--un": True},
           dudup=True,
           dudupOP=None,
           extractMethyOP={
                "--no_overlap": True,
                "--report": True,
                "--no_header": True,
                "--gzip": True,
                "--bedGraph": True,
                "--zero_based": True,
           },
           methyRegion=None,
           armCNV=False,
           CNV=False,
           fragProfile=False,
           OCF=False,
           report=False,
           verbose=False,
           box=True)

• caseFolder: str, input case fastq file folder path. Setting this parameter means disable fastq1 and fastq2.

• ctrlFolder: str, input control fastq file folder path. Setting this parameter means disable fastq1 and fastq2.

• caseFq1: list, case fastq1 files.

• caseFq2: list, case fastq2 files.

• ctrlFq1: list, control fastq1 files.

• ctrlFq2: list, control fastq2 files.

• caseAdapter1: list, adapters for case fastq1 files, if idAdapter is True, this paramter will be disabled.

• caseAdapter2: list, adapters control for case fastq2 files, if idAdapter is True, this paramter will be disabled.

• ctrlAdapter1: list, adapters control for fastq1 files, if idAdapter is True, this paramter will be disabled.

• ctrlAdapter2: list, adapters for fastq2 files, if idAdapter is True, this paramter will be disabled.

• fastqcOP: Other parameters used for fastqc, please see class “fastqc”.

• idAdapter: Ture or False, identify adapters or not. This module is not for single end data.

• idAdOP: Other parameters used for AdapterRemoval, please see class “identifyAdapter”.

  If idAdapter is False, this paramter will be disabled.

• rmAdapter: Ture or False, remove adapters or not.

• rmAdOP: Other parameters used for AdapterRemoval, please see class “adapterremoval”.

  Default: {“–qualitybase”: 33, “–gzip”: True}. If rmAdapter is False, this paramter will be disabled.

• bismarkOP: Other parameters used for Bismark, please see class “bismark”.

  Default: {“-q”: True, “–phred33-quals”: True, “–bowtie2”: True, “–un”: True,}.

• dudup: Ture or False, remove duplicates for bismark results or not.

• dudupOP: Other parameters used for bismark_deduplicate, please see class “bismark_deduplicate”.

  If dudup is False, this paramter will be disabled.

• extractMethyOP: Other parameters used for bismark_methylation_extractor, please see class “bismark_methylation_extractor”.

  Default: {“–no_overlap”: True, “–report”: True, “–no_header”: True, “–gzip”: True,

  “–bedGraph”: True, “–zero_based”: True,}

• methyRegion: Bed file contains methylation related regions.

• armCNV: Compute arm level CNV or not.

• CNV: Compute CNV or not. If True, CNV will be computed for 3 group: case VS reference,

  control VS reference, case VS control.

• fragProfile: Compute basic fragProfile(long short fragement statistics) or not. This module is not for single end data.

• deconvolution: Compute tissue proportion for each sample or not.

• OCF: Compute OCF or not.

• report: Generate user report or not.

• verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

• box: output will be a box class. that mean the the results can be specified using ‘.’,

  otherwise, the results will be saved as dict.

Example usage:

from cfDNApipe import *

pipeConfigure2(
    threads=20,
    genome="hg19",
    refdir="path_to_genome/hg19_bismark",
    outdir="path_to_output/pipeline-WGBS-comp",
    data="WGBS",
    type="paired",
    JavaMem="8G",
    case="cancer",
    ctrl="normal",
    build=True,
)

case, ctrl, comp = cfDNAWGBS2(
    caseFolder="path_to_fastqs/raw/case",
    ctrlFolder="path_to_fastqs/raw/ctrl",
    caseName="cancer",
    ctrlName="tumor",
    idAdapter=True,
    rmAdapter=True,
    dudup=True,
    armCNV=True,
    CNV=True,
    fragProfile=True,
    deconvolution=True,
    OCF=True,
    verbose=True,
)