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Report generated at 2020-07-09 21:35:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	83123602	134911976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80526261	131561749
Mapped(QC-failed)	0	0
% Mapped	96.8800	97.5200
Paired	83123602	134911976
Paired(QC-failed)	0	0
Read1	41561801	67455988
Read1(QC-failed)	0	0
Read2	41561801	67455988
Read2(QC-failed)	0	0
Properly Paired	79512842	129326590
Properly Paired(QC-failed)	0	0
% Properly Paired	95.6600	95.8600
With itself	80231959	130892791
With itself(QC-failed)	0	0
Singletons	294302	668958
Singletons(QC-failed)	0	0
% Singleton	0.3500	0.5000
Diff. Chroms	460351	887675
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	36289585	56598486
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	156738	240623
Paired Opt. Dupes	1371	1949
% Dupes/100	0.0043	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36287407	56554856
Distinct Read Pairs	36130680	56314799
One Read Pair	35974577	56075865
Two Read Pairs	155483	237833
NRF = Distinct/Total	0.9957	0.9958
PBC1 = OnePair/Distinct	0.9957	0.9958
PBC2 = OnePair/TwoPair	231.3731	235.7783

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	72265694	112715726
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72265694	112715726
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72265694	112715726
Paired(QC-failed)	0	0
Read1	36132847	56357863
Read1(QC-failed)	0	0
Read2	36132847	56357863
Read2(QC-failed)	0	0
Properly Paired	72265694	112715726
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72265694	112715726
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	117214
Np	0
N optimal	117214
N conservative	117214
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.	175
Corr. Est. Fragment Len.	0.1833
Phantom Peak	50
Corr. Phantom Peak	0.1870
Argmin. Corr.	1500
Min. Corr.	0.1751
NSC	1.0471
RSC	0.6923

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	0.2101

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	0.2345
AUC	0.4952
CHANCE divergence	0.1204
Elbow Point	0.0000
JS Distance	0.6537
Synthetic AUC	0.5058
Synthetic Elbow Point	0.1877
Synthetic JS Distance	0.3499