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Report generated at 2022-01-07 00:02:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	196598482	192176210
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	191335217	189111268
Mapped(QC-failed)	0	0
% Mapped	97.3200	98.4100
Paired	196598482	192176210
Paired(QC-failed)	0	0
Read1	98299241	96088105
Read1(QC-failed)	0	0
Read2	98299241	96088105
Read2(QC-failed)	0	0
Properly Paired	189029381	185501344
Properly Paired(QC-failed)	0	0
% Properly Paired	96.1500	96.5300
With itself	189857228	188039217
With itself(QC-failed)	0	0
Singletons	1477989	1072051
Singletons(QC-failed)	0	0
% Singleton	0.7500	0.5600
Diff. Chroms	126403	189579
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	81700505	81981435
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4667504	827349
Paired Opt. Dupes	6370	5795
% Dupes/100	0.0571	0.0101

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	81681280	81951776
Distinct Read Pairs	77015595	81129218
One Read Pair	72616624	80347579
Two Read Pairs	4165451	763930
NRF = Distinct/Total	0.9429	0.9900
PBC1 = OnePair/Distinct	0.9429	0.9904
PBC2 = OnePair/TwoPair	17.4331	105.1766

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	154066002	162308172
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	154066002	162308172
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	154066002	162308172
Paired(QC-failed)	0	0
Read1	77033001	81154086
Read1(QC-failed)	0	0
Read2	77033001	81154086
Read2(QC-failed)	0	0
Properly Paired	154066002	162308172
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	154066002	162308172
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	138564
Np	0
N optimal	138564
N conservative	138564
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.	0.1903
Phantom Peak	50
Corr. Phantom Peak	0.2038
Argmin. Corr.	1500
Min. Corr.	0.1805
NSC	1.0544
RSC	0.4205

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	0.4342

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	0.2140
AUC	0.4967
CHANCE divergence	0.0947
Elbow Point	0.0000
JS Distance	0.7551
Synthetic AUC	0.5013
Synthetic Elbow Point	0.2605
Synthetic JS Distance	0.4008