QC Report

	general
Report generated at	2019-10-18 03:43:47
Title	h1_sox2
Description	Cut-n-run sample h1_sox2
Pipeline version	dev-v0.1.0
Pipeline type	cut_n_run
Genome	hg19
Paired-end per replicate	[True]
Aligner	bowtie2
Peak caller	macs2
Control paired-end per replicate	[True]

Alignment quality metrics

SAMstat (raw BAM)

	rep1
Total Reads	22564698
Total Reads (QC-failed)	0
Duplicate Reads	0
Duplicate Reads (QC-failed)	0
Mapped Reads	21444893
Mapped Reads (QC-failed)	0
% Mapped Reads	95.0
Paired Reads	22564698
Paired Reads (QC-failed)	0
Read1	11282349
Read1 (QC-failed)	0
Read2	11282349
Read2 (QC-failed)	0
Properly Paired Reads	20411220
Properly Paired Reads (QC-failed)	0
% Properly Paired Reads	90.5
With itself	21147502
With itself (QC-failed)	0
Singletons	297391
Singletons (QC-failed)	0
% Singleton	1.3
Diff. Chroms	536232
Diff. Chroms (QC-failed)	0

Marking duplicates (filtered BAMs)

	rep1
Unpaired Reads	0
Paired Reads	9047226
Unmapped Reads	0
Unpaired Duplicate Reads	0
Paired Duplicate Reads	284658
Paired Optical Duplicate Reads	0
% Duplicate Reads	3.1464

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

Fraction of mitochondrial reads

	rep1
Rm = Number of Non-mitochondrial Reads	20432885
Rn = Number of Mitochondrial Reads	1147614
Rm/(Rn+Rm) = Frac. of mitochondrial reads	0.0531782884167785

SAMstat (filtered/deduped BAM)

	rep1
Total Reads	17211324
Total Reads (QC-failed)	0
Duplicate Reads	0
Duplicate Reads (QC-failed)	0
Mapped Reads	17211324
Mapped Reads (QC-failed)	0
% Mapped Reads	100.0
Paired Reads	17211324
Paired Reads (QC-failed)	0
Read1	8605662
Read1 (QC-failed)	0
Read2	8605662
Read2 (QC-failed)	0
Properly Paired Reads	17211324
Properly Paired Reads (QC-failed)	0
% Properly Paired Reads	100.0
With itself	17211324
With itself (QC-failed)	0
Singletons	0
Singletons (QC-failed)	0
% Singleton	0.0
Diff. Chroms	0
Diff. Chroms (QC-failed)	0

Filtered and duplicates removed

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1
Total Fragments	8659787
Distinct Fragments	8605662
Positions with Two Read	44655
NRF = Distinct/Total	0.99375
PBC1 = OneRead/Distinct	0.994517
PBC2 = OneRead/TwoRead	191.657821

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	0	0
N1	29947	7454
Np	0	0
N optimal	29947	7454
N conservative	29947	7454
Optimal Set	rep1-pr1_vs_rep1-pr2	rep1-pr1_vs_rep1-pr2
Conservative Set	rep1-pr1_vs_rep1-pr2	rep1-pr1_vs_rep1-pr2
Rescue Ratio	0.0	0.0
Self Consistency Ratio	1.0	1.0
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
Number of peaks	40227

Top 300000 raw peaks from macs2 with p-val threshold 0.01

Peak calling statistics

Peak region size

	rep1	idr_opt	overlap_opt
Min size	73.0	73.0	73.0
25 percentile	84.0	241.0	104.0
50 percentile (median)	129.0	352.5	164.0
75 percentile	225.0	517.0	271.0
Max size	1662.0	1662.0	1662.0
Mean	188.9270639122977	408.2856184598873	221.9621331018132

Enrichment / Signal-to-noise ratio

Jensen-Shannon distance

	rep1
AUC	0.20686551153361005
Synthetic AUC	0.4830210285926876
X-intercept	0.28659535279965925
Synthetic X-intercept	6.582458436130745e-29
Elbow Point	0.607969714604544
Synthetic Elbow Point	0.5251922240327144
Synthetic JS Distance	0.28558157897613906

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for macs2 raw peaks

	rep1	rep1-pr1	rep1-pr2
Fraction of Reads in Peaks	0.05245546478585843	0.0705192697551914	0.0709638607698048

FRiP for overlap peaks

	rep1-pr1_vs_rep1-pr2
Fraction of Reads in Peaks	0.04528623132072814

FRiP for IDR peaks

	rep1-pr1_vs_rep1-pr2
Fraction of Reads in Peaks	0.019207993527981925

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