Quality Control

The Following example shows how to perform fragment length analysis. For up- and down-stream relationship, please see “Up Down Stream Flowchart” part.

fragment length Example usage

from cfDNApipe import *
import glob
import pysam

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

case_bed = ["./HCC/GM1100.bed", "./HCC/H195.bed"]
ctrl_bed = ["./Healthy/C309.bed", "./Healthy/C310.bed"]

res_fraglenplot_comp = fraglenplot_comp(
   casebedInput=case_bed, ctrlbedInput=ctrl_bed, caseupstream=True, verbose=verbose)