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Report generated at 2020-11-26 08:55:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	162640378	193594802
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	160421937	187969057
Mapped(QC-failed)	0	0
% Mapped	98.6400	97.0900
Paired	162640378	193594802
Paired(QC-failed)	0	0
Read1	81320189	96797401
Read1(QC-failed)	0	0
Read2	81320189	96797401
Read2(QC-failed)	0	0
Properly Paired	158920829	184287983
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7100	95.1900
With itself	159517390	185784698
With itself(QC-failed)	0	0
Singletons	904547	2184359
Singletons(QC-failed)	0	0
% Singleton	0.5600	1.1300
Diff. Chroms	294397	610670
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	71296382	78211821
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1664607	539110
Paired Opt. Dupes	15815	19807
% Dupes/100	0.0233	0.0069

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	71280944	77646644
Distinct Read Pairs	69616733	77172156
One Read Pair	67986532	76701136
Two Read Pairs	1597068	467668
NRF = Distinct/Total	0.9767	0.9939
PBC1 = OnePair/Distinct	0.9766	0.9939
PBC2 = OnePair/TwoPair	42.5696	164.0077

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	139263550	155345422
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139263550	155345422
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	139263550	155345422
Paired(QC-failed)	0	0
Read1	69631775	77672711
Read1(QC-failed)	0	0
Read2	69631775	77672711
Read2(QC-failed)	0	0
Properly Paired	139263550	155345422
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	139263550	155345422
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	173587
Np	0
N optimal	173587
N conservative	173587
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.	150
Corr. Est. Fragment Len.	0.2505
Phantom Peak	50
Corr. Phantom Peak	0.2348
Argmin. Corr.	1500
Min. Corr.	0.1963
NSC	1.2762
RSC	1.4088

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	0.5016

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	0.1566
AUC	0.4966
CHANCE divergence	0.1214
Elbow Point	0.0000
JS Distance	0.8003
Synthetic AUC	0.5010
Synthetic Elbow Point	0.4148
Synthetic JS Distance	0.5068