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Report generated at 2021-10-23 17:09:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	225089062	140797568
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	215075595	138331903
Mapped(QC-failed)	0	0
% Mapped	95.5500	98.2500
Paired	225089062	140797568
Paired(QC-failed)	0	0
Read1	112544531	70398784
Read1(QC-failed)	0	0
Read2	112544531	70398784
Read2(QC-failed)	0	0
Properly Paired	203402110	130482644
Properly Paired(QC-failed)	0	0
% Properly Paired	90.3700	92.6700
With itself	209969093	136981110
With itself(QC-failed)	0	0
Singletons	5106502	1350793
Singletons(QC-failed)	0	0
% Singleton	2.2700	0.9600
Diff. Chroms	3924573	4662721
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	79062252	54667780
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	12644422	4758897
Paired Opt. Dupes	20843	8500
% Dupes/100	0.1599	0.0871

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	79048816	54581914
Distinct Read Pairs	66406310	49831729
One Read Pair	55506045	45411889
Two Read Pairs	9377745	4111745
NRF = Distinct/Total	0.8401	0.9130
PBC1 = OnePair/Distinct	0.8359	0.9113
PBC2 = OnePair/TwoPair	5.9189	11.0444

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	132835660	99817766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	132835660	99817766
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	132835660	99817766
Paired(QC-failed)	0	0
Read1	66417830	49908883
Read1(QC-failed)	0	0
Read2	66417830	49908883
Read2(QC-failed)	0	0
Properly Paired	132835660	99817766
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	132835660	99817766
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	105568
Np	0
N optimal	105568
N conservative	105568
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.	115
Corr. Est. Fragment Len.	0.1793
Phantom Peak	50
Corr. Phantom Peak	0.2029
Argmin. Corr.	1500
Min. Corr.	0.1732
NSC	1.0358
RSC	0.2083

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	0.0672

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	0.3043
AUC	0.4957
CHANCE divergence	0.1032
Elbow Point	0.0000
JS Distance	0.5524
Synthetic AUC	0.5045
Synthetic Elbow Point	0.0921
Synthetic JS Distance	0.2389