Basic Data Processing

Basic data processing part involves steps from raw fastq file to BAM/BED file procedure. For up- and down-stream relationship, please see “Up Down Stream Flowchart” part. For more demos, please see here.

WGBS Example usage

from cfDNApipe import *

pipeConfigure(
   threads=60,
   genome="hg19",
   refdir=r"path_to_reference/hg19_bismark",
   outdir=r"path_to_output/WGBS",
   data="WGBS",
   type="paired",
   JavaMem="10g",
   build=True,
)


verbose = False

res_inputprocess = inputprocess(inputFolder="path_to_fastq")

res_fastqc = fastqc(upstream=res_inputprocess, verbose=verbose)

res_identifyAdapter = identifyAdapter(upstream=res_inputprocess, verbose=verbose)

res_adapterremoval = adapterremoval(upstream=res_identifyAdapter, verbose=verbose)

res_bismark = bismark(upstream=res_adapterremoval, verbose=verbose)

res_deduplicate = bismark_deduplicate(upstream=res_bismark, verbose=verbose)

WGS Example usage

from cfDNApipe import *

pipeConfigure(
   threads=20,
   genome="hg19",
   refdir=r"path_to_reference/hg19_bowtie2",
   outdir=r"path_to_output/WGS",
   data="WGS",
   type="paired",
   JavaMem="10G",
   build=True,
)

verbose = False

res_inputprocess = inputprocess(inputFolder="path_to_fastq")

res_fastqc = fastqc(upstream=res_inputprocess, verbose=verbose)

res_identifyAdapter = identifyAdapter(upstream=res_inputprocess, verbose=verbose)

res_adapterremoval = adapterremoval(upstream=res_identifyAdapter, verbose=verbose)

res_bowtie2 = bowtie2(upstream=res_adapterremoval, verbose=verbose)

res_bamsort = bamsort(upstream=res_bowtie2, verbose=verbose)

pre-set pipeline Example usage

from cfDNApipe import *

pipeConfigure2(
   threads=120,
   genome="hg38",
   refdir="/home/zhangwei/Genome/hg38_bismark",
   outdir="/opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-compare",
   data="WGBS",
   type="paired",
   JavaMem="10G",
   case="cancer",
   ctrl="normal",
   build=True,
)

# fragProfile is set to False because the demo data is too small to get valid values
a, b = cfDNAWGBS2(
   caseFolder="/opt/tsinghua/zhangwei/Pipeline_test/WGBS-compare/case",
   ctrlFolder="/opt/tsinghua/zhangwei/Pipeline_test/WGBS-compare/ctrl",
   caseName="cancer",
   ctrlName="normal",
   idAdapter=True,
   rmAdapter=True,
   dudup=True,
   armCNV=True,
   CNV=True,
   fragProfile=False,
   deconvolution=True,
   OCF=True,
   report=True,
   verbose=False,
)

DMR = computeDMR(caseupstream=a.calculate_methyl, ctrlupstream=b.calculate_methyl)