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Report generated at 2020-11-26 22:54:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	105245102	334658014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101503707	328702336
Mapped(QC-failed)	0	0
% Mapped	96.4500	98.2200
Paired	105245102	334658014
Paired(QC-failed)	0	0
Read1	52622551	167329007
Read1(QC-failed)	0	0
Read2	52622551	167329007
Read2(QC-failed)	0	0
Properly Paired	98952193	320102484
Properly Paired(QC-failed)	0	0
% Properly Paired	94.0200	95.6500
With itself	100978533	326658529
With itself(QC-failed)	0	0
Singletons	525174	2043807
Singletons(QC-failed)	0	0
% Singleton	0.5000	0.6100
Diff. Chroms	162752	620372
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	44332343	141663705
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1754885	1830718
Paired Opt. Dupes	3888	10233
% Dupes/100	0.0396	0.0129

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44284311	141095473
Distinct Read Pairs	42531764	139340732
One Read Pair	40834141	137631421
Two Read Pairs	1644208	1682298
NRF = Distinct/Total	0.9604	0.9876
PBC1 = OnePair/Distinct	0.9601	0.9877
PBC2 = OnePair/TwoPair	24.8351	81.8116

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	85154916	279665974
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85154916	279665974
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	85154916	279665974
Paired(QC-failed)	0	0
Read1	42577458	139832987
Read1(QC-failed)	0	0
Read2	42577458	139832987
Read2(QC-failed)	0	0
Properly Paired	85154916	279665974
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	85154916	279665974
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	121646
Np	0
N optimal	121646
N conservative	121646
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.	125
Corr. Est. Fragment Len.	0.1802
Phantom Peak	50
Corr. Phantom Peak	0.1874
Argmin. Corr.	1500
Min. Corr.	0.1724
NSC	1.0454
RSC	0.5219

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	0.1435

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	0.2899
AUC	0.4956
CHANCE divergence	0.0992
Elbow Point	0.0000
JS Distance	0.5904
Synthetic AUC	0.5012
Synthetic Elbow Point	0.1739
Synthetic JS Distance	0.2718