QC Report

	general
Report generated at	2021-11-01 20:02:50
Title	cbf1_nexus
Description	chipnexus data
Pipeline version	v1.2.0
Pipeline type	ChIP-nexus
Genome	sacCer3
Aligner	bowtie
Sequencing endedness	{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}}
Peak caller	macs2

Replication quality metrics

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

	rep1	rep2
Number of peaks	1646	1515

Top 500000 raw peaks from macs2 with p-val threshold 0.01

	rep1	rep2	idr_opt	overlap_opt
Min size	150.0	150.0	163.0	151.0
25 percentile	216.0	223.5	612.25	336.0
50 percentile (median)	344.5	341.0	1030.0	542.0
75 percentile	653.5	662.0	1404.25	1035.5
Max size	2980.0	3023.0	3060.0	3060.0
Mean	544.1130012150668	495.34059405940593	1057.5524193548388	730.133730834753

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.28217380053363966	0.3460822346017398	0.25047849268099487	0.32496081117988757	0.25004457516319245	0.3242944569846263	0.3249795985728468	0.29995782965799944	0.30020715839552525

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.29395259856092504	0.251255599508332	0.32394771072322637	0.3021989594395551

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.24370793337925944	0.1788761851865293	0.23097662841690272	0.21089547246105378

For macs2 raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates