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Report generated at 2020-06-10 04:28:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52303818	96892848
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51849807	95177950
Mapped(QC-failed)	0	0
% Mapped	99.1300	98.2300
Paired	52303818	96892848
Paired(QC-failed)	0	0
Read1	26151909	48446424
Read1(QC-failed)	0	0
Read2	26151909	48446424
Read2(QC-failed)	0	0
Properly Paired	51485630	93194227
Properly Paired(QC-failed)	0	0
% Properly Paired	98.4400	96.1800
With itself	51557739	94492205
With itself(QC-failed)	0	0
Singletons	292068	685745
Singletons(QC-failed)	0	0
% Singleton	0.5600	0.7100
Diff. Chroms	15435	166792
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	23787499	40925788
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	189402	246444
Paired Opt. Dupes	1835	1204
% Dupes/100	0.0080	0.0060

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23778748	40844131
Distinct Read Pairs	23589634	40626962
One Read Pair	23404830	40418355
Two Read Pairs	181000	204968
NRF = Distinct/Total	0.9920	0.9947
PBC1 = OnePair/Distinct	0.9922	0.9949
PBC2 = OnePair/TwoPair	129.3085	197.1935

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	47196194	81358688
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	47196194	81358688
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	47196194	81358688
Paired(QC-failed)	0	0
Read1	23598097	40679344
Read1(QC-failed)	0	0
Read2	23598097	40679344
Read2(QC-failed)	0	0
Properly Paired	47196194	81358688
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	47196194	81358688
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	94254
Np	0
N optimal	94254
N conservative	94254
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.	150
Corr. Est. Fragment Len.	0.1959
Phantom Peak	45
Corr. Phantom Peak	0.1866
Argmin. Corr.	1500
Min. Corr.	0.1719
NSC	1.1397
RSC	1.6297

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	0.3314

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	0.1967
AUC	0.4941
CHANCE divergence	0.1430
Elbow Point	0.0000
JS Distance	0.7281
Synthetic AUC	0.4974
Synthetic Elbow Point	0.2887
Synthetic JS Distance	0.4156