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Report generated at 2021-10-10 08:00:45

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	155640082	168628396
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127694382	163343908
Mapped(QC-failed)	0	0
% Mapped	82.0400	96.8700
Paired	155640082	168628396
Paired(QC-failed)	0	0
Read1	77820041	84314198
Read1(QC-failed)	0	0
Read2	77820041	84314198
Read2(QC-failed)	0	0
Properly Paired	126471226	159133434
Properly Paired(QC-failed)	0	0
% Properly Paired	81.2600	94.3700
With itself	126923180	162244869
With itself(QC-failed)	0	0
Singletons	771202	1099039
Singletons(QC-failed)	0	0
% Singleton	0.5000	0.6500
Diff. Chroms	264881	2067566
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	56912652	66322288
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	17717446	4095947
Paired Opt. Dupes	28783	41316
% Dupes/100	0.3113	0.0618

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	56911706	66307420
Distinct Read Pairs	39194573	62212428
One Read Pair	26410021	58305094
Two Read Pairs	9112246	3728896
NRF = Distinct/Total	0.6887	0.9382
PBC1 = OnePair/Distinct	0.6738	0.9372
PBC2 = OnePair/TwoPair	2.8983	15.6360

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	78390412	124452682
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78390412	124452682
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78390412	124452682
Paired(QC-failed)	0	0
Read1	39195206	62226341
Read1(QC-failed)	0	0
Read2	39195206	62226341
Read2(QC-failed)	0	0
Properly Paired	78390412	124452682
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78390412	124452682
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	42063
Np	0
N optimal	42063
N conservative	42063
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.	190
Corr. Est. Fragment Len.	0.4295
Phantom Peak	55
Corr. Phantom Peak	0.3913
Argmin. Corr.	1500
Min. Corr.	0.1867
NSC	2.3009
RSC	1.1866

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	0.7020

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	0.0772
AUC	0.4944
CHANCE divergence	0.2077
Elbow Point	0.0000
JS Distance	0.9364
Synthetic AUC	0.5058
Synthetic Elbow Point	0.6316
Synthetic JS Distance	0.6805