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Report generated at 2020-07-10 12:53:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	107483056	112753966
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106177963	109868487
Mapped(QC-failed)	0	0
% Mapped	98.7900	97.4400
Paired	107483056	112753966
Paired(QC-failed)	0	0
Read1	53741528	56376983
Read1(QC-failed)	0	0
Read2	53741528	56376983
Read2(QC-failed)	0	0
Properly Paired	86869972	87661066
Properly Paired(QC-failed)	0	0
% Properly Paired	80.8200	77.7500
With itself	105294574	108182157
With itself(QC-failed)	0	0
Singletons	883389	1686330
Singletons(QC-failed)	0	0
% Singleton	0.8200	1.5000
Diff. Chroms	16433144	16951047
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	40140444	38372389
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	630750	558393
Paired Opt. Dupes	3102	2534
% Dupes/100	0.0157	0.0146

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40104368	38298911
Distinct Read Pairs	39478684	37755269
One Read Pair	38869652	37227219
Two Read Pairs	594293	517899
NRF = Distinct/Total	0.9844	0.9858
PBC1 = OnePair/Distinct	0.9846	0.9860
PBC2 = OnePair/TwoPair	65.4049	71.8812

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	79019388	75627992
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79019388	75627992
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	79019388	75627992
Paired(QC-failed)	0	0
Read1	39509694	37813996
Read1(QC-failed)	0	0
Read2	39509694	37813996
Read2(QC-failed)	0	0
Properly Paired	79019388	75627992
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	79019388	75627992
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	229607
Np	0
N optimal	229607
N conservative	229607
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.	0.1782
Phantom Peak	55
Corr. Phantom Peak	0.1754
Argmin. Corr.	1500
Min. Corr.	0.1678
NSC	1.0622
RSC	1.3690

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	0.3124

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	0.2244
AUC	0.4954
CHANCE divergence	0.1165
Elbow Point	0.0000
JS Distance	0.7040
Synthetic AUC	0.5037
Synthetic Elbow Point	0.2017
Synthetic JS Distance	0.3663