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Report generated at 2020-05-21 00:59:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	184008744	134902134
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	181609339	132183014
Mapped(QC-failed)	0	0
% Mapped	98.7000	97.9800
Paired	184008744	134902134
Paired(QC-failed)	0	0
Read1	92004372	67451067
Read1(QC-failed)	0	0
Read2	92004372	67451067
Read2(QC-failed)	0	0
Properly Paired	173774926	128630862
Properly Paired(QC-failed)	0	0
% Properly Paired	94.4400	95.3500
With itself	180397262	131319824
With itself(QC-failed)	0	0
Singletons	1212077	863190
Singletons(QC-failed)	0	0
% Singleton	0.6600	0.6400
Diff. Chroms	219108	216771
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	75481971	56502483
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3342797	559124
Paired Opt. Dupes	1796	1089
% Dupes/100	0.0443	0.0099

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	75480863	56501008
Distinct Read Pairs	72138117	55941912
One Read Pair	68951523	55416619
Two Read Pairs	3047058	510347
NRF = Distinct/Total	0.9557	0.9901
PBC1 = OnePair/Distinct	0.9558	0.9906
PBC2 = OnePair/TwoPair	22.6289	108.5862

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	144278348	111886718
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	144278348	111886718
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	144278348	111886718
Paired(QC-failed)	0	0
Read1	72139174	55943359
Read1(QC-failed)	0	0
Read2	72139174	55943359
Read2(QC-failed)	0	0
Properly Paired	144278348	111886718
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	144278348	111886718
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	206409
Np	0
N optimal	206409
N conservative	206409
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.	145
Corr. Est. Fragment Len.	0.1810
Phantom Peak	50
Corr. Phantom Peak	0.1829
Argmin. Corr.	1500
Min. Corr.	0.1740
NSC	1.0399
RSC	0.7844

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	0.1318

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	0.2511
AUC	0.4966
CHANCE divergence	0.1125
Elbow Point	0.0000
JS Distance	0.5822
Synthetic AUC	0.5046
Synthetic Elbow Point	0.1586
Synthetic JS Distance	0.3342