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Report generated at 2020-07-15 04:28:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	72578386	155229270
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	69540392	150942743
Mapped(QC-failed)	0	0
% Mapped	95.8100	97.2400
Paired	72578386	155229270
Paired(QC-failed)	0	0
Read1	36289193	77614635
Read1(QC-failed)	0	0
Read2	36289193	77614635
Read2(QC-failed)	0	0
Properly Paired	68822882	148607764
Properly Paired(QC-failed)	0	0
% Properly Paired	94.8300	95.7300
With itself	69193565	150154922
With itself(QC-failed)	0	0
Singletons	346827	787821
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5100
Diff. Chroms	164436	787266
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	30606109	64735106
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	269923	274206
Paired Opt. Dupes	9702	1163
% Dupes/100	0.0088	0.0042

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30593367	64655208
Distinct Read Pairs	30323599	64382549
One Read Pair	30056155	64112121
Two Read Pairs	265137	268358
NRF = Distinct/Total	0.9912	0.9958
PBC1 = OnePair/Distinct	0.9912	0.9958
PBC2 = OnePair/TwoPair	113.3608	238.9052

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	60672372	128921800
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60672372	128921800
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	60672372	128921800
Paired(QC-failed)	0	0
Read1	30336186	64460900
Read1(QC-failed)	0	0
Read2	30336186	64460900
Read2(QC-failed)	0	0
Properly Paired	60672372	128921800
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	60672372	128921800
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	34779
Np	0
N optimal	34779
N conservative	34779
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.	200
Corr. Est. Fragment Len.	0.2170
Phantom Peak	50
Corr. Phantom Peak	0.2250
Argmin. Corr.	1500
Min. Corr.	0.1783
NSC	1.2174
RSC	0.8292

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	0.2404

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	0.2372
AUC	0.4948
CHANCE divergence	0.1148
Elbow Point	0.0000
JS Distance	0.6776
Synthetic AUC	0.5034
Synthetic Elbow Point	0.2674
Synthetic JS Distance	0.3752