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Report generated at 2020-06-05 22:35:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	107042608	102780848
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101956301	100831339
Mapped(QC-failed)	0	0
% Mapped	95.2500	98.1000
Paired	107042608	102780848
Paired(QC-failed)	0	0
Read1	53521304	51390424
Read1(QC-failed)	0	0
Read2	53521304	51390424
Read2(QC-failed)	0	0
Properly Paired	99190262	99231317
Properly Paired(QC-failed)	0	0
% Properly Paired	92.6600	96.5500
With itself	100178965	99905065
With itself(QC-failed)	0	0
Singletons	1777336	926274
Singletons(QC-failed)	0	0
% Singleton	1.6600	0.9000
Diff. Chroms	170277	333186
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	36745784	43402346
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6363056	817520
Paired Opt. Dupes	3198	3763
% Dupes/100	0.1732	0.0188

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36744972	43363402
Distinct Read Pairs	30382040	42547036
One Read Pair	25135528	41765324
Two Read Pairs	4343239	759025
NRF = Distinct/Total	0.8268	0.9812
PBC1 = OnePair/Distinct	0.8273	0.9816
PBC2 = OnePair/TwoPair	5.7873	55.0250

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	60765456	85169652
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60765456	85169652
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	60765456	85169652
Paired(QC-failed)	0	0
Read1	30382728	42584826
Read1(QC-failed)	0	0
Read2	30382728	42584826
Read2(QC-failed)	0	0
Properly Paired	60765456	85169652
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	60765456	85169652
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	161431
Np	0
N optimal	161431
N conservative	161431
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.	115
Corr. Est. Fragment Len.	0.1891
Phantom Peak	50
Corr. Phantom Peak	0.2249
Argmin. Corr.	1500
Min. Corr.	0.1789
NSC	1.0570
RSC	0.2221

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	0.1800

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	0.2086
AUC	0.4948
CHANCE divergence	0.1834
Elbow Point	0.0000
JS Distance	0.6370
Synthetic AUC	0.5092
Synthetic Elbow Point	0.1561
Synthetic JS Distance	0.3667