QC Report

	general
Report generated at	2019-10-22 17:33:37
Title	h1 ctcf cutrun auto a
Description	This is a cut n run data for h1 ctcf with auto a control.
Pipeline version	dev-v0.1.0
Pipeline type	cut_n_run
Genome	hg19
Paired-end per replicate	[True, True]
Aligner	bowtie2
Peak caller	macs2
Control paired-end per replicate	[True, True]

Alignment quality metrics

SAMstat (raw BAM)

	rep1	rep2
Total Reads	16270578	16068156
Total Reads (QC-failed)	0	0
Duplicate Reads	0	0
Duplicate Reads (QC-failed)	0	0
Mapped Reads	15320454	15377563
Mapped Reads (QC-failed)	0	0
% Mapped Reads	94.19999999999999	95.7
Paired Reads	16270578	16068156
Paired Reads (QC-failed)	0	0
Read1	8135289	8034078
Read1 (QC-failed)	0	0
Read2	8135289	8034078
Read2 (QC-failed)	0	0
Properly Paired Reads	15035496	15113712
Properly Paired Reads (QC-failed)	0	0
% Properly Paired Reads	92.4	94.1
With itself	15187904	15255914
With itself (QC-failed)	0	0
Singletons	132550	121649
Singletons (QC-failed)	0	0
% Singleton	0.8	0.8
Diff. Chroms	112545	105493
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAMs)

	rep1	rep2
Unpaired Reads	0	0
Paired Reads	6974459	7018816
Unmapped Reads	0	0
Unpaired Duplicate Reads	0	0
Paired Duplicate Reads	1864514	1598947
Paired Optical Duplicate Reads	0	0
% Duplicate Reads	26.7335	22.780900000000003

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	rep2
Rm = Number of Non-mitochondrial Reads	14978102	15033209
Rn = Number of Mitochondrial Reads	392120	394996
Rm/(Rn+Rm) = Frac. of mitochondrial reads	0.02551166795118509	0.02560220064485791

SAMstat (filtered/deduped BAM)

	rep1	rep2
Total Reads	10108304	10724558
Total Reads (QC-failed)	0	0
Duplicate Reads	0	0
Duplicate Reads (QC-failed)	0	0
Mapped Reads	10108304	10724558
Mapped Reads (QC-failed)	0	0
% Mapped Reads	100.0	100.0
Paired Reads	10108304	10724558
Paired Reads (QC-failed)	0	0
Read1	5054152	5362279
Read1 (QC-failed)	0	0
Read2	5054152	5362279
Read2 (QC-failed)	0	0
Properly Paired Reads	10108304	10724558
Properly Paired Reads (QC-failed)	0	0
% Properly Paired Reads	100.0	100.0
With itself	10108304	10724558
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

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2
Total Fragments	6840705	6883945
Distinct Fragments	5054156	5362286
Positions with Two Read	992324	906514
NRF = Distinct/Total	0.738836	0.778955
PBC1 = OneRead/Distinct	0.740603	0.785402
PBC2 = OneRead/TwoRead	3.772076	4.645873

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	75870	45726
N1	73925	42632
N2	74077	41649
Np	74192	45558
N optimal	75870	45726
N conservative	75870	45726
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0226169937459564	1.0036876070064533
Self Consistency Ratio	1.00205613797768	1.0236020072510745
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	99059	96342

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

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	243.0	243.0	243.0	243.0
25 percentile	321.0	323.0	722.0	430.0
50 percentile (median)	547.0	547.5	989.0	711.0
75 percentile	990.0	964.0	1343.0	1112.0
Max size	5288.0	5210.0	5365.0	5365.0
Mean	729.1375241017979	717.4189865271636	1093.6416262082842	840.7859101093976

Enrichment / Signal-to-noise ratio

Jensen-Shannon distance

	rep1	rep2
AUC	0.07402649425386351	0.07529275480782728
Synthetic AUC	0.47786683511140704	0.47852711468616993
X-intercept	0.613731219115156	0.6045320102471188
Synthetic X-intercept	8.475887066080954e-17	7.113487026695306e-18
Elbow Point	0.7613465241989189	0.7506954401921435
Synthetic Elbow Point	0.49555897726913356	0.5237477916163796
Synthetic JS Distance	0.4543478689939197	0.45745915738309195

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	0.43965060805452627	0.43534390881190627	0.4592250094575707	0.46432189292614334	0.4587885366328516	0.46432094717953826	0.4217985507704126	0.4327717974830537	0.4325151707446793

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	0.40861174043201554	0.4105807462854303	0.4108173036128855	0.40647991620162416

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	0.34881721964077717	0.3367100949872501	0.3369156099486804	0.3481428523838923

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