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Report generated at 2022-01-06 11:28:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120257936	129938162
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114537435	127236885
Mapped(QC-failed)	0	0
% Mapped	95.2400	97.9200
Paired	120257936	129938162
Paired(QC-failed)	0	0
Read1	60128968	64969081
Read1(QC-failed)	0	0
Read2	60128968	64969081
Read2(QC-failed)	0	0
Properly Paired	111931928	124171709
Properly Paired(QC-failed)	0	0
% Properly Paired	93.0800	95.5600
With itself	113216823	126465025
With itself(QC-failed)	0	0
Singletons	1320612	771860
Singletons(QC-failed)	0	0
% Singleton	1.1000	0.5900
Diff. Chroms	101261	239097
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	41060910	54765194
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	740584	445948
Paired Opt. Dupes	1572	1420
% Dupes/100	0.0180	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41047551	54643833
Distinct Read Pairs	40307800	54251204
One Read Pair	39607911	53876689
Two Read Pairs	679439	366311
NRF = Distinct/Total	0.9820	0.9928
PBC1 = OnePair/Distinct	0.9826	0.9931
PBC2 = OnePair/TwoPair	58.2950	147.0791

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	80640652	108638492
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80640652	108638492
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80640652	108638492
Paired(QC-failed)	0	0
Read1	40320326	54319246
Read1(QC-failed)	0	0
Read2	40320326	54319246
Read2(QC-failed)	0	0
Properly Paired	80640652	108638492
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80640652	108638492
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	125051
Np	0
N optimal	125051
N conservative	125051
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.	-10
Corr. Est. Fragment Len.	0.1971
Phantom Peak	50
Corr. Phantom Peak	0.2200
Argmin. Corr.	1500
Min. Corr.	0.1848
NSC	1.0666
RSC	0.3486

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	0.3019

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	0.2235
AUC	0.4955
CHANCE divergence	0.1136
Elbow Point	0.0000
JS Distance	0.6809
Synthetic AUC	0.5017
Synthetic Elbow Point	0.1987
Synthetic JS Distance	0.3721