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Report generated at 2020-06-05 19:21:45

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104776114	106180416
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95950398	98634603
Mapped(QC-failed)	0	0
% Mapped	91.5800	92.8900
Paired	104776114	106180416
Paired(QC-failed)	0	0
Read1	52388057	53090208
Read1(QC-failed)	0	0
Read2	52388057	53090208
Read2(QC-failed)	0	0
Properly Paired	88876813	91384608
Properly Paired(QC-failed)	0	0
% Properly Paired	84.8300	86.0700
With itself	89762530	92607302
With itself(QC-failed)	0	0
Singletons	6187868	6027301
Singletons(QC-failed)	0	0
% Singleton	5.9100	5.6800
Diff. Chroms	424156	792823
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	34849817	37372803
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8111208	355863
Paired Opt. Dupes	3020	3080
% Dupes/100	0.2327	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34849237	37337759
Distinct Read Pairs	26738137	36982560
One Read Pair	20400682	36645193
Two Read Pairs	4953808	328167
NRF = Distinct/Total	0.7673	0.9905
PBC1 = OnePair/Distinct	0.7630	0.9909
PBC2 = OnePair/TwoPair	4.1182	111.6663

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	53477218	74033880
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53477218	74033880
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	53477218	74033880
Paired(QC-failed)	0	0
Read1	26738609	37016940
Read1(QC-failed)	0	0
Read2	26738609	37016940
Read2(QC-failed)	0	0
Properly Paired	53477218	74033880
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	53477218	74033880
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	37804
Np	0
N optimal	37804
N conservative	37804
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.	120
Corr. Est. Fragment Len.	0.1680
Phantom Peak	50
Corr. Phantom Peak	0.1876
Argmin. Corr.	1500
Min. Corr.	0.1611
NSC	1.0427
RSC	0.2594

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	0.0183

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	0.2990
AUC	0.4944
CHANCE divergence	0.1110
Elbow Point	0.0000
JS Distance	0.5436
Synthetic AUC	0.5031
Synthetic Elbow Point	0.0496
Synthetic JS Distance	0.2404