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Report generated at 2020-05-20 19:16:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	122227292	136200922
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116171083	132760866
Mapped(QC-failed)	0	0
% Mapped	95.0500	97.4700
Paired	122227292	136200922
Paired(QC-failed)	0	0
Read1	61113646	68100461
Read1(QC-failed)	0	0
Read2	61113646	68100461
Read2(QC-failed)	0	0
Properly Paired	114378442	130688000
Properly Paired(QC-failed)	0	0
% Properly Paired	93.5800	95.9500
With itself	115540008	132096613
With itself(QC-failed)	0	0
Singletons	631075	664253
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.4900
Diff. Chroms	636348	663242
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	50605666	56907844
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	342807	250818
Paired Opt. Dupes	2501	2178
% Dupes/100	0.0068	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50600916	56865752
Distinct Read Pairs	50258154	56615485
One Read Pair	49917754	56366456
Two Read Pairs	338051	247819
NRF = Distinct/Total	0.9932	0.9956
PBC1 = OnePair/Distinct	0.9932	0.9956
PBC2 = OnePair/TwoPair	147.6634	227.4501

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	100525718	113314052
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100525718	113314052
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	100525718	113314052
Paired(QC-failed)	0	0
Read1	50262859	56657026
Read1(QC-failed)	0	0
Read2	50262859	56657026
Read2(QC-failed)	0	0
Properly Paired	100525718	113314052
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	100525718	113314052
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	226019
Np	0
N optimal	226019
N conservative	226019
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.	135
Corr. Est. Fragment Len.	0.1953
Phantom Peak	50
Corr. Phantom Peak	0.2079
Argmin. Corr.	1500
Min. Corr.	0.1855
NSC	1.0526
RSC	0.4356

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	0.3972

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	0.1958
AUC	0.4959
CHANCE divergence	0.1146
Elbow Point	0.0000
JS Distance	0.7357
Synthetic AUC	0.5054
Synthetic Elbow Point	0.2542
Synthetic JS Distance	0.4223