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Report generated at 2019-10-27 04:04:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	293261232	195514228
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	290035024	192553965
Mapped(QC-failed)	0	0
% Mapped	98.9000	98.4900
Paired	293261232	195514228
Paired(QC-failed)	0	0
Read1	146630616	97757114
Read1(QC-failed)	0	0
Read2	146630616	97757114
Read2(QC-failed)	0	0
Properly Paired	283361797	184591444
Properly Paired(QC-failed)	0	0
% Properly Paired	96.6200	94.4100
With itself	288509823	190690270
With itself(QC-failed)	0	0
Singletons	1525201	1863695
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.9500
Diff. Chroms	3587750	4309653
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	118966352	77004602
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	14682660	6090607
Paired Opt. Dupes	29944	12922
% Dupes/100	0.1234	0.0791

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	118965480	76983195
Distinct Read Pairs	104282908	70894296
One Read Pair	91103547	65158036
Two Read Pairs	11815512	5405511
NRF = Distinct/Total	0.8766	0.9209
PBC1 = OnePair/Distinct	0.8736	0.9191
PBC2 = OnePair/TwoPair	7.7105	12.0540

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	208567384	141827990
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	208567384	141827990
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	208567384	141827990
Paired(QC-failed)	0	0
Read1	104283692	70913995
Read1(QC-failed)	0	0
Read2	104283692	70913995
Read2(QC-failed)	0	0
Properly Paired	208567384	141827990
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	208567384	141827990
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	214093
Np	0
N optimal	214093
N conservative	214093
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.	160
Corr. Est. Fragment Len.	0.1807
Phantom Peak	50
Corr. Phantom Peak	0.1869
Argmin. Corr.	1500
Min. Corr.	0.1771
NSC	1.0200
RSC	0.3618

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	0.2610

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	0.2469
AUC	0.4965
CHANCE divergence	0.1017
Elbow Point	0.0000
JS Distance	0.6207
Synthetic AUC	0.5059
Synthetic Elbow Point	0.2127
Synthetic JS Distance	0.3428