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Report generated at 2020-05-21 11:28:20

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	163878380	192499798
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108973826	188890798
Mapped(QC-failed)	0	0
% Mapped	66.5000	98.1300
Paired	163878380	192499798
Paired(QC-failed)	0	0
Read1	81939190	96249899
Read1(QC-failed)	0	0
Read2	81939190	96249899
Read2(QC-failed)	0	0
Properly Paired	106122733	186811687
Properly Paired(QC-failed)	0	0
% Properly Paired	64.7600	97.0500
With itself	107143184	188072528
With itself(QC-failed)	0	0
Singletons	1830642	818270
Singletons(QC-failed)	0	0
% Singleton	1.1200	0.4300
Diff. Chroms	271655	400341
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	42420143	81972176
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	364966	587245
Paired Opt. Dupes	2313	4247
% Dupes/100	0.0086	0.0072

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42417823	81931652
Distinct Read Pairs	42052878	81345140
One Read Pair	41697003	80765524
Two Read Pairs	348694	573498
NRF = Distinct/Total	0.9914	0.9928
PBC1 = OnePair/Distinct	0.9915	0.9929
PBC2 = OnePair/TwoPair	119.5805	140.8297

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	84110354	162769862
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84110354	162769862
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84110354	162769862
Paired(QC-failed)	0	0
Read1	42055177	81384931
Read1(QC-failed)	0	0
Read2	42055177	81384931
Read2(QC-failed)	0	0
Properly Paired	84110354	162769862
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84110354	162769862
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	205053
Np	0
N optimal	205053
N conservative	205053
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.	0.1845
Phantom Peak	50
Corr. Phantom Peak	0.2389
Argmin. Corr.	1500
Min. Corr.	0.1682
NSC	1.0966
RSC	0.2297

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	0.1753

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	0.2278
AUC	0.4956
CHANCE divergence	0.1506
Elbow Point	0.0000
JS Distance	0.6211
Synthetic AUC	0.4984
Synthetic Elbow Point	0.1427
Synthetic JS Distance	0.3502