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Report generated at 2021-01-20 18:54:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	91062316	334658014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90199379	328702336
Mapped(QC-failed)	0	0
% Mapped	99.0500	98.2200
Paired	91062316	334658014
Paired(QC-failed)	0	0
Read1	45531158	167329007
Read1(QC-failed)	0	0
Read2	45531158	167329007
Read2(QC-failed)	0	0
Properly Paired	89658261	320102484
Properly Paired(QC-failed)	0	0
% Properly Paired	98.4600	95.6500
With itself	89980049	326658529
With itself(QC-failed)	0	0
Singletons	219330	2043807
Singletons(QC-failed)	0	0
% Singleton	0.2400	0.6100
Diff. Chroms	146926	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	41024803	141663705
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	13913395	1830718
Paired Opt. Dupes	6695	10233
% Dupes/100	0.3391	0.0129

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40978104	141095473
Distinct Read Pairs	27080967	139340732
One Read Pair	17500563	137631421
Two Read Pairs	6451409	1682298
NRF = Distinct/Total	0.6609	0.9876
PBC1 = OnePair/Distinct	0.6462	0.9877
PBC2 = OnePair/TwoPair	2.7127	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	54222816	279665974
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	54222816	279665974
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	54222816	279665974
Paired(QC-failed)	0	0
Read1	27111408	139832987
Read1(QC-failed)	0	0
Read2	27111408	139832987
Read2(QC-failed)	0	0
Properly Paired	54222816	279665974
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	54222816	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	108200
Np	0
N optimal	108200
N conservative	108200
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.	245
Corr. Est. Fragment Len.	0.1770
Phantom Peak	50
Corr. Phantom Peak	0.1747
Argmin. Corr.	1500
Min. Corr.	0.1613
NSC	1.0978
RSC	1.1684

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	0.3269

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	0.2058
AUC	0.4945
CHANCE divergence	0.1398
Elbow Point	0.0000
JS Distance	0.7020
Synthetic AUC	0.4949
Synthetic Elbow Point	0.3147
Synthetic JS Distance	0.3964