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Report generated at 2019-10-30 13:51:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	108730046	143714130
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105721253	141651275
Mapped(QC-failed)	0	0
% Mapped	97.2300	98.5600
Paired	108730046	143714130
Paired(QC-failed)	0	0
Read1	54365023	71857065
Read1(QC-failed)	0	0
Read2	54365023	71857065
Read2(QC-failed)	0	0
Properly Paired	101648928	136021403
Properly Paired(QC-failed)	0	0
% Properly Paired	93.4900	94.6500
With itself	104083422	140589137
With itself(QC-failed)	0	0
Singletons	1637831	1062138
Singletons(QC-failed)	0	0
% Singleton	1.5100	0.7400
Diff. Chroms	1780641	3177801
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	43183504	56070460
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5078377	6270525
Paired Opt. Dupes	39589	24403
% Dupes/100	0.1176	0.1118

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43182588	55969749
Distinct Read Pairs	38104312	49713031
One Read Pair	33529604	44051001
Two Read Pairs	4116503	5120262
NRF = Distinct/Total	0.8824	0.8882
PBC1 = OnePair/Distinct	0.8799	0.8861
PBC2 = OnePair/TwoPair	8.1452	8.6033

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	76210254	99599870
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76210254	99599870
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76210254	99599870
Paired(QC-failed)	0	0
Read1	38105127	49799935
Read1(QC-failed)	0	0
Read2	38105127	49799935
Read2(QC-failed)	0	0
Properly Paired	76210254	99599870
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76210254	99599870
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	130963
Np	0
N optimal	130963
N conservative	130963
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.	180
Corr. Est. Fragment Len.	0.2175
Phantom Peak	50
Corr. Phantom Peak	0.2169
Argmin. Corr.	1500
Min. Corr.	0.2082
NSC	1.0447
RSC	1.0661

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	0.7546

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	0.0708
AUC	0.4943
CHANCE divergence	0.4459
Elbow Point	0.0000
JS Distance	0.8257
Synthetic AUC	0.4986
Synthetic Elbow Point	0.4540
Synthetic JS Distance	0.5879