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Report generated at 2019-10-31 18:38:27

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	94220072	226039766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92062605	215792208
Mapped(QC-failed)	0	0
% Mapped	97.7100	95.4700
Paired	94220072	226039766
Paired(QC-failed)	0	0
Read1	47110036	113019883
Read1(QC-failed)	0	0
Read2	47110036	113019883
Read2(QC-failed)	0	0
Properly Paired	90829334	149610145
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4000	66.1900
With itself	91484086	208550392
With itself(QC-failed)	0	0
Singletons	578519	7241816
Singletons(QC-failed)	0	0
% Singleton	0.6100	3.2000
Diff. Chroms	99805	32459107
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	38131801	41767173
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	28611136	7918501
Paired Opt. Dupes	9470	11777
% Dupes/100	0.7503	0.1896

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38129179	41734528
Distinct Read Pairs	9520032	33823168
One Read Pair	2427213	27301386
Two Read Pairs	1693668	5377365
NRF = Distinct/Total	0.2497	0.8104
PBC1 = OnePair/Distinct	0.2550	0.8072
PBC2 = OnePair/TwoPair	1.4331	5.0771

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	19041330	67697344
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	19041330	67697344
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	19041330	67697344
Paired(QC-failed)	0	0
Read1	9520665	33848672
Read1(QC-failed)	0	0
Read2	9520665	33848672
Read2(QC-failed)	0	0
Properly Paired	19041330	67697344
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	19041330	67697344
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	28092
Np	0
N optimal	28092
N conservative	28092
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.	155
Corr. Est. Fragment Len.	0.0810
Phantom Peak	50
Corr. Phantom Peak	0.0860
Argmin. Corr.	1500
Min. Corr.	0.0750
NSC	1.0800
RSC	0.5437

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	0.1014

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	0.2179
AUC	0.4886
CHANCE divergence	0.2578
Elbow Point	0.0000
JS Distance	0.6298
Synthetic AUC	0.5043
Synthetic Elbow Point	0.1266
Synthetic JS Distance	0.3001