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Report generated at 2020-05-21 17:06:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	233005316	192478142
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	194663047	185401012
Mapped(QC-failed)	0	0
% Mapped	83.5400	96.3200
Paired	233005316	192478142
Paired(QC-failed)	0	0
Read1	116502658	96239071
Read1(QC-failed)	0	0
Read2	116502658	96239071
Read2(QC-failed)	0	0
Properly Paired	191182621	183168625
Properly Paired(QC-failed)	0	0
% Properly Paired	82.0500	95.1600
With itself	192957070	184250860
With itself(QC-failed)	0	0
Singletons	1705977	1150152
Singletons(QC-failed)	0	0
% Singleton	0.7300	0.6000
Diff. Chroms	921573	298242
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

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

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	82697345	78445518
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	743456	555253
Paired Opt. Dupes	2462	2096
% Dupes/100	0.0090	0.0071

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	82694201	78441301
Distinct Read Pairs	81950769	77886084
One Read Pair	81216018	77336819
Two Read Pairs	726346	543707
NRF = Distinct/Total	0.9910	0.9929
PBC1 = OnePair/Distinct	0.9910	0.9929
PBC2 = OnePair/TwoPair	111.8145	142.2399

Mitochondrial reads are filtered out.

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

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	ctl1
Total	163907778	155780530
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	163907778	155780530
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	163907778	155780530
Paired(QC-failed)	0	0
Read1	81953889	77890265
Read1(QC-failed)	0	0
Read2	81953889	77890265
Read2(QC-failed)	0	0
Properly Paired	163907778	155780530
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	163907778	155780530
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	256961
Np	0
N optimal	256961
N conservative	256961
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping 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'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	105
Corr. Est. Fragment Len.	0.1901
Phantom Peak	50
Corr. Phantom Peak	0.2168
Argmin. Corr.	1500
Min. Corr.	0.1792
NSC	1.0607
RSC	0.2897

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.2683

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.2475
AUC	0.4968
CHANCE divergence	0.0967
Elbow Point	0.0000
JS Distance	0.6560
Synthetic AUC	0.4981
Synthetic Elbow Point	0.1615
Synthetic JS Distance	0.3419