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Report generated at 2019-11-03 19:30:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	109052300	213968900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107794203	211195024
Mapped(QC-failed)	0	0
% Mapped	98.8500	98.7000
Paired	109052300	213968900
Paired(QC-failed)	0	0
Read1	54526150	106984450
Read1(QC-failed)	0	0
Read2	54526150	106984450
Read2(QC-failed)	0	0
Properly Paired	106488540	206798914
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6500	96.6500
With itself	107269075	210073494
With itself(QC-failed)	0	0
Singletons	525128	1121530
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5200
Diff. Chroms	482220	2031909
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	49111864	91477404
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3513949	2315030
Paired Opt. Dupes	16312	43440
% Dupes/100	0.0716	0.0253

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49109035	91372844
Distinct Read Pairs	45595293	89062444
One Read Pair	42283905	86800060
Two Read Pairs	3119001	2218941
NRF = Distinct/Total	0.9284	0.9747
PBC1 = OnePair/Distinct	0.9274	0.9746
PBC2 = OnePair/TwoPair	13.5569	39.1178

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	91195830	178324748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91195830	178324748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	91195830	178324748
Paired(QC-failed)	0	0
Read1	45597915	89162374
Read1(QC-failed)	0	0
Read2	45597915	89162374
Read2(QC-failed)	0	0
Properly Paired	91195830	178324748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	91195830	178324748
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	82065
Np	0
N optimal	82065
N conservative	82065
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.	195
Corr. Est. Fragment Len.	0.2216
Phantom Peak	50
Corr. Phantom Peak	0.2206
Argmin. Corr.	1500
Min. Corr.	0.1991
NSC	1.1132
RSC	1.0462

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	0.5613

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	0.1501
AUC	0.4957
CHANCE divergence	0.1209
Elbow Point	0.0000
JS Distance	0.8571
Synthetic AUC	0.5069
Synthetic Elbow Point	0.4567
Synthetic JS Distance	0.5227