QC Report

	general
Report generated at	2021-11-01 22:41:30
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	4636	4520
Total Reads (QC-failed)	0	0
Duplicate Reads	0	0
Duplicate Reads (QC-failed)	0	0
Mapped Reads	4636	4520
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	4636	4520
Total Reads (QC-failed)	0	0
Duplicate Reads	0	0
Duplicate Reads (QC-failed)	0	0
Mapped Reads	4636	4520
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	3176868	2156752
Distinct Fragments	3176868	2156752
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	1178	495
N1	1090	478
N2	1139	364
Np	1314	305
N optimal	1314	495
N conservative	1178	495
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1154499151103565	1.6229508196721312
Self Consistency Ratio	1.044954128440367	1.3131868131868132
Reproducibility Test	pass	pass

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	1882	1766

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	150.0	150.0	150.0	152.0
25 percentile	213.25	211.0	629.5	321.25
50 percentile (median)	331.5	317.0	1042.0	514.5
75 percentile	620.0	599.75	1439.0	967.0
Max size	3172.0	3054.0	3176.0	3176.0
Mean	529.1944739638682	473.9597961494904	1071.270707070707	705.4322678843226

Enrichment / Signal-to-noise ratio

TSS enrichment (filtered/deduped BAM)

	rep1	rep2
TSS enrichment	1.6974291762028348	2.1279864394261963

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	0.30861323240050975	0.27582253573751053
Synthetic AUC	0.4984464155613839	0.4981536004958232
X-intercept	0.04313493790245636	0.04341039470164835
Synthetic X-intercept	0.0	0.0
Elbow Point	0.7296211870191981	0.7903973364525156
Synthetic Elbow Point	0.5022146933160728	0.500747608525378
Synthetic JS Distance	0.28997884682542796	0.3571896960727411

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	0.2981521422986413	0.3609742798430232	0.26566794717312775	0.33784505589887015	0.26686094606385913	0.33993801790841044	0.33757035559338683	0.3116071261169712	0.31276356395843724

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	0.30424439686366855	0.2657076088776745	0.33673319881006253	0.3131871036931765

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	0.2448592138172573	0.21301797871362613	0.2601819773437094	0.21263700826080598

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