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Report generated at 2022-01-07 01:40:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	176498180	201652566
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	175029863	198032065
Mapped(QC-failed)	0	0
% Mapped	99.1700	98.2000
Paired	176498180	201652566
Paired(QC-failed)	0	0
Read1	88249090	100826283
Read1(QC-failed)	0	0
Read2	88249090	100826283
Read2(QC-failed)	0	0
Properly Paired	163340212	194936556
Properly Paired(QC-failed)	0	0
% Properly Paired	92.5400	96.6700
With itself	174110798	196867125
With itself(QC-failed)	0	0
Singletons	919065	1164940
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.5800
Diff. Chroms	110816	328067
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	77149350	84633399
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7643910	1125235
Paired Opt. Dupes	4140	1306
% Dupes/100	0.0991	0.0133

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	77139304	84626173
Distinct Read Pairs	69496748	83501515
One Read Pair	62676193	82459535
Two Read Pairs	6133413	999176
NRF = Distinct/Total	0.9009	0.9867
PBC1 = OnePair/Distinct	0.9019	0.9875
PBC2 = OnePair/TwoPair	10.2188	82.5275

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	139010880	167016328
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139010880	167016328
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	139010880	167016328
Paired(QC-failed)	0	0
Read1	69505440	83508164
Read1(QC-failed)	0	0
Read2	69505440	83508164
Read2(QC-failed)	0	0
Properly Paired	139010880	167016328
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	139010880	167016328
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	159793
Np	0
N optimal	159793
N conservative	159793
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.	145
Corr. Est. Fragment Len.	0.2178
Phantom Peak	45
Corr. Phantom Peak	0.1926
Argmin. Corr.	1500
Min. Corr.	0.1808
NSC	1.2045
RSC	3.1531

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	0.6691

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	0.1131
AUC	0.4965
CHANCE divergence	0.1617
Elbow Point	0.0000
JS Distance	0.8200
Synthetic AUC	0.5062
Synthetic Elbow Point	0.4469
Synthetic JS Distance	0.5744