QC Report

	general
Report generated at	2021-10-10 13:17:30
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

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2
Total Reads	2603	2506
Total Reads (QC-failed)	0	0
Duplicate Reads	0	0
Duplicate Reads (QC-failed)	0	0
Mapped Reads	2603	2506
Mapped Reads (QC-failed)	0	0
% Mapped Reads	100.0	100.0
Paired Reads	0	0
Paired Reads (QC-failed)	0	0
Read1	0	0
Read1 (QC-failed)	0	0
Read2	0	0
Read2 (QC-failed)	0	0
Properly Paired Reads	0	0
Properly Paired Reads (QC-failed)	0	0
% Properly Paired Reads	0.0	0.0
With itself	0	0
With itself (QC-failed)	0	0
Singletons	0	0
Singletons (QC-failed)	0	0
% Singleton	0.0	0.0
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

SAMstat (filtered/deduped BAM)

	rep1	rep2
Total Reads	2603	2506
Total Reads (QC-failed)	0	0
Duplicate Reads	0	0
Duplicate Reads (QC-failed)	0	0
Mapped Reads	2603	2506
Mapped Reads (QC-failed)	0	0
% Mapped Reads	100.0	100.0
Paired Reads	0	0
Paired Reads (QC-failed)	0	0
Read1	0	0
Read1 (QC-failed)	0	0
Read2	0	0
Read2 (QC-failed)	0	0
Properly Paired Reads	0	0
Properly Paired Reads (QC-failed)	0	0
% Properly Paired Reads	0.0	0.0
With itself	0	0
With itself (QC-failed)	0	0
Singletons	0	0
Singletons (QC-failed)	0	0
% Singleton	0.0	0.0
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2
Total Fragments	6050	5435
Distinct Fragments	6050	5435
Positions with Two Read	None	None
NRF = Distinct/Total	1.0	1.0
PBC1 = OneRead/Distinct	None	None
PBC2 = OneRead/TwoRead	None	None

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	424	15
N1	647	4
N2	567	17
Np	976	28
N optimal	976	28
N conservative	424	15
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	2.30188679245283	1.8666666666666667
Self Consistency Ratio	1.1410934744268078	4.25
Reproducibility Test	borderline	borderline

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'

Number of raw peaks

	rep1	rep2
Number of peaks	3254	3028

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

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	121.0	150.0	150.0	150.0
25 percentile	150.0	150.0	256.5	150.0
50 percentile (median)	150.0	150.0	297.5	150.0
75 percentile	150.0	150.0	356.5	215.25
Max size	544.0	862.0	506.0	609.0
Mean	159.54148740012292	162.22952443857332	302.5	193.8360655737705

Enrichment / Signal-to-noise ratio

TSS enrichment (filtered/deduped BAM)

	rep1	rep2
TSS enrichment	1.7015764119474113	2.257571076565005

Open chromatin assays should show enrichment in open chromatin sites, such as TSS's. An average TSS enrichment in human (hg19) is above 6. A strong TSS enrichment is above 10. For other references please see https://www.encodeproject.org/atac-seq/

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.05668062256386068	0.04867837721347659
Synthetic AUC	0.4643326964400867	0.46311827012030043
X-intercept	0.825505728960885	0.8459877518767286
Synthetic X-intercept	2.3875736545339655e-06	6.17597860514504e-06
Elbow Point	0.8325780323982616	0.8519182141446069
Synthetic Elbow Point	0.49027091710559134	0.4912734670178043
Synthetic JS Distance	0.18356448957783203	0.21241707838029256

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.8639669421487604	0.904691812327507	0.9537190082644628	0.9668874172185431	0.9514049586776859	0.9657710710342289	0.7141488898563344	0.8608741076092634	0.8573667711598746

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.1825859817152808	0.3160330578512397	0.3560257589696412	0.31658685241619505

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.03204179364388333	0.009421487603305785	0.04949402023919043	0.04588593818023509

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