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)