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Report generated at 2020-06-06 06:17:27

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	128861364	94272842
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127995333	92659557
Mapped(QC-failed)	0	0
% Mapped	99.3300	98.2900
Paired	128861364	94272842
Paired(QC-failed)	0	0
Read1	64430682	47136421
Read1(QC-failed)	0	0
Read2	64430682	47136421
Read2(QC-failed)	0	0
Properly Paired	127389082	91574742
Properly Paired(QC-failed)	0	0
% Properly Paired	98.8600	97.1400
With itself	127698206	92304558
With itself(QC-failed)	0	0
Singletons	297127	354999
Singletons(QC-failed)	0	0
% Singleton	0.2300	0.3800
Diff. Chroms	104421	370286
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	57878718	40575988
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8615120	1257392
Paired Opt. Dupes	4966	3763
% Dupes/100	0.1488	0.0310

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	57852761	40180957
Distinct Read Pairs	49241909	38989114
One Read Pair	42028150	37836528
Two Read Pairs	6037735	1116568
NRF = Distinct/Total	0.8512	0.9703
PBC1 = OnePair/Distinct	0.8535	0.9704
PBC2 = OnePair/TwoPair	6.9609	33.8865

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	98527196	78637192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98527196	78637192
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	98527196	78637192
Paired(QC-failed)	0	0
Read1	49263598	39318596
Read1(QC-failed)	0	0
Read2	49263598	39318596
Read2(QC-failed)	0	0
Properly Paired	98527196	78637192
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	98527196	78637192
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	187628
Np	0
N optimal	187628
N conservative	187628
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.	165
Corr. Est. Fragment Len.	0.1693
Phantom Peak	50
Corr. Phantom Peak	0.1731
Argmin. Corr.	1500
Min. Corr.	0.1659
NSC	1.0206
RSC	0.4740

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	0.1770

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	0.2717
AUC	0.4959
CHANCE divergence	0.1074
Elbow Point	0.0000
JS Distance	0.6282
Synthetic AUC	0.4980
Synthetic Elbow Point	0.1399
Synthetic JS Distance	0.2886