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Report generated at 2019-11-03 11:19:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120973616	155278814
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	118918201	152204810
Mapped(QC-failed)	0	0
% Mapped	98.3000	98.0200
Paired	120973616	155278814
Paired(QC-failed)	0	0
Read1	60486808	77639407
Read1(QC-failed)	0	0
Read2	60486808	77639407
Read2(QC-failed)	0	0
Properly Paired	117504535	149315055
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1300	96.1600
With itself	118331817	151298295
With itself(QC-failed)	0	0
Singletons	586384	906515
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5800
Diff. Chroms	256983	1045401
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	52723326	66029859
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5926645	1524871
Paired Opt. Dupes	9383	14661
% Dupes/100	0.1124	0.0231

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52719689	65968445
Distinct Read Pairs	46793480	64445697
One Read Pair	41423540	62945345
Two Read Pairs	4858548	1479272
NRF = Distinct/Total	0.8876	0.9769
PBC1 = OnePair/Distinct	0.8852	0.9767
PBC2 = OnePair/TwoPair	8.5259	42.5516

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	93593362	129009976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	93593362	129009976
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	93593362	129009976
Paired(QC-failed)	0	0
Read1	46796681	64504988
Read1(QC-failed)	0	0
Read2	46796681	64504988
Read2(QC-failed)	0	0
Properly Paired	93593362	129009976
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	93593362	129009976
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	26480
Np	0
N optimal	26480
N conservative	26480
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.	0.2273
Phantom Peak	50
Corr. Phantom Peak	0.2231
Argmin. Corr.	1500
Min. Corr.	0.1674
NSC	1.3577
RSC	1.0763

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	0.2472

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	0.2638
AUC	0.4958
CHANCE divergence	0.0984
Elbow Point	0.0000
JS Distance	0.6949
Synthetic AUC	0.5064
Synthetic Elbow Point	0.2918
Synthetic JS Distance	0.3606