QC Report

	general
Report generated at	2019-10-21 00:40:39
Title	h1 oct4 cutrun
Description	This is a cut n run data for h1 oct4.
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	25232058	18152438
Total Reads (QC-failed)	0	0
Duplicate Reads	0	0
Duplicate Reads (QC-failed)	0	0
Mapped Reads	23825888	16411382
Mapped Reads (QC-failed)	0	0
% Mapped Reads	94.39999999999999	90.4
Paired Reads	25232058	18152438
Paired Reads (QC-failed)	0	0
Read1	12616029	9076219
Read1 (QC-failed)	0	0
Read2	12616029	9076219
Read2 (QC-failed)	0	0
Properly Paired Reads	23006872	15985094
Properly Paired Reads (QC-failed)	0	0
% Properly Paired Reads	91.2	88.1
With itself	23560800	16164128
With itself (QC-failed)	0	0
Singletons	265088	247254
Singletons (QC-failed)	0	0
% Singleton	1.0999999999999999	1.4000000000000001
Diff. Chroms	352452	103285
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAMs)

	rep1	rep2
Unpaired Reads	0	0
Paired Reads	9597750	6807264
Unmapped Reads	0	0
Unpaired Duplicate Reads	0	0
Paired Duplicate Reads	1301907	1725975
Paired Optical Duplicate Reads	0	0
% Duplicate Reads	13.564699999999998	25.3549

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	19789209	14773119
Rn = Number of Mitochondrial Reads	4597195	1862893
Rm/(Rn+Rm) = Frac. of mitochondrial reads	0.18851467399621527	0.11197954173151595

SAMstat (filtered/deduped BAM)

	rep1	rep2
Total Reads	15891128	9785264
Total Reads (QC-failed)	0	0
Duplicate Reads	0	0
Duplicate Reads (QC-failed)	0	0
Mapped Reads	15891128	9785264
Mapped Reads (QC-failed)	0	0
% Mapped Reads	100.0	100.0
Paired Reads	15891128	9785264
Paired Reads (QC-failed)	0	0
Read1	7945564	4892632
Read1 (QC-failed)	0	0
Read2	7945564	4892632
Read2 (QC-failed)	0	0
Properly Paired Reads	15891128	9785264
Properly Paired Reads (QC-failed)	0	0
% Properly Paired Reads	100.0	100.0
With itself	15891128	9785264
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	8025456	6161792
Distinct Fragments	7945564	4892638
Positions with Two Read	66120	851536
NRF = Distinct/Total	0.990045	0.794028
PBC1 = OneRead/Distinct	0.991442	0.787425
PBC2 = OneRead/TwoRead	119.140396	4.524278

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	2833	936
N1	2378	465
N2	7931	1480
Np	4040	1242
N optimal	4040	1242
N conservative	2833	936
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.4260501235439464	1.3269230769230769
Self Consistency Ratio	3.33515559293524	3.182795698924731
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	4466	22882

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	500.0	500.0	502.0	500.0
25 percentile	530.25	521.0	761.25	607.0
50 percentile (median)	621.0	595.0	932.0	737.0
75 percentile	793.0	749.0	1196.75	935.0
Max size	3372.0	4756.0	4453.0	4453.0
Mean	719.4180474697716	693.2671095183988	1048.8582930756843	831.5925742574258

Enrichment / Signal-to-noise ratio

Jensen-Shannon distance

	rep1	rep2
AUC	0.24381500287301647	0.18825980265990153
Synthetic AUC	0.48230413041339265	0.4774740650980266
X-intercept	0.25615797041454436	0.4173241101265291
Synthetic X-intercept	1.4542802125367884e-26	3.3345397088789085e-16
Elbow Point	0.5748385638835061	0.5747565709348996
Synthetic Elbow Point	0.5002553079683713	0.5211533434732087
Synthetic JS Distance	0.21510750978598786	0.2142757515214338

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	0.009056059456572245	0.04730674614399775	0.025830891299849827	0.07362519805290894	0.025735743869157682	0.07350195150585616	0.01476056293267372	0.01910650063295497	0.018991375423774493

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	0.009149649997554174	0.006351657352454778	0.02768356581897024	0.0118446158634749

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	0.004885187918925681	0.0024584787184396225	0.010668082128392244	0.006041152510835634

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