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Report generated at 2021-10-10 00:14:49

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98175632	140797568
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91537771	138331903
Mapped(QC-failed)	0	0
% Mapped	93.2400	98.2500
Paired	98175632	140797568
Paired(QC-failed)	0	0
Read1	49087816	70398784
Read1(QC-failed)	0	0
Read2	49087816	70398784
Read2(QC-failed)	0	0
Properly Paired	88069511	130482644
Properly Paired(QC-failed)	0	0
% Properly Paired	89.7100	92.6700
With itself	89342921	136981110
With itself(QC-failed)	0	0
Singletons	2194850	1350793
Singletons(QC-failed)	0	0
% Singleton	2.2400	0.9600
Diff. Chroms	780113	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	38292050	54667780
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8711880	4758897
Paired Opt. Dupes	7460	8500
% Dupes/100	0.2275	0.0871

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38281803	54581914
Distinct Read Pairs	29572178	49831729
One Read Pair	22566444	45411889
Two Read Pairs	5600507	4111745
NRF = Distinct/Total	0.7725	0.9130
PBC1 = OnePair/Distinct	0.7631	0.9113
PBC2 = OnePair/TwoPair	4.0294	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	59160340	99817766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59160340	99817766
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	59160340	99817766
Paired(QC-failed)	0	0
Read1	29580170	49908883
Read1(QC-failed)	0	0
Read2	29580170	49908883
Read2(QC-failed)	0	0
Properly Paired	59160340	99817766
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	59160340	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	89366
Np	0
N optimal	89366
N conservative	89366
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.	185
Corr. Est. Fragment Len.	0.1960
Phantom Peak	50
Corr. Phantom Peak	0.1943
Argmin. Corr.	1500
Min. Corr.	0.1702
NSC	1.1516
RSC	1.0735

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	0.3629

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	0.1941
AUC	0.4935
CHANCE divergence	0.1335
Elbow Point	0.0000
JS Distance	0.7631
Synthetic AUC	0.5022
Synthetic Elbow Point	0.3333
Synthetic JS Distance	0.4270