QC Report

Outputs quality control report from given bam files.

Usually as a first step after receiving bam files, we want to do a quality check and assess our data. This code generates a PDF report of important QC statistics for modified base data from Nanopore sequencing.

1. Python option

import dimelo as dm

# first we specify the locations of our bam files
bam = "winnowmap_guppy_merge_subset.bam"
sampleName = "CTCF"
outdir = "./out"

# next we run the "qc_report" function
dm.qc_report(bam, sampleName, outdir)
# now our output directory will have a file called "CTCF_qc_report.pdf"

2. Command line option

dimelo-qc-report -f winnowmap_guppy_merge_subset.bam -s CTCF -o ./out

Output