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Report generated at 2020-07-10 01:59:52

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	171761676	109897006
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	169911484	108231726
Mapped(QC-failed)	0	0
% Mapped	98.9200	98.4800
Paired	171761676	109897006
Paired(QC-failed)	0	0
Read1	85880838	54948503
Read1(QC-failed)	0	0
Read2	85880838	54948503
Read2(QC-failed)	0	0
Properly Paired	168205621	105268015
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9300	95.7900
With itself	169191318	107714777
With itself(QC-failed)	0	0
Singletons	720166	516949
Singletons(QC-failed)	0	0
% Singleton	0.4200	0.4700
Diff. Chroms	123109	292990
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	77609296	46292526
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1458264	315764
Paired Opt. Dupes	4270	2945
% Dupes/100	0.0188	0.0068

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	77521147	46198469
Distinct Read Pairs	76083567	45905006
One Read Pair	74694888	45622153
Two Read Pairs	1345683	278233
NRF = Distinct/Total	0.9815	0.9936
PBC1 = OnePair/Distinct	0.9817	0.9938
PBC2 = OnePair/TwoPair	55.5070	163.9710

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	152302064	91953524
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	152302064	91953524
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	152302064	91953524
Paired(QC-failed)	0	0
Read1	76151032	45976762
Read1(QC-failed)	0	0
Read2	76151032	45976762
Read2(QC-failed)	0	0
Properly Paired	152302064	91953524
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	152302064	91953524
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	260616
Np	0
N optimal	260616
N conservative	260616
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.	145
Corr. Est. Fragment Len.	0.1814
Phantom Peak	45
Corr. Phantom Peak	0.1793
Argmin. Corr.	1500
Min. Corr.	0.1701
NSC	1.0667
RSC	1.2320

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	0.3841

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	0.2269
AUC	0.4967
CHANCE divergence	0.1016
Elbow Point	0.0000
JS Distance	0.7405
Synthetic AUC	0.4997
Synthetic Elbow Point	0.2436
Synthetic JS Distance	0.3739