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Report generated at 2021-03-19 05:08:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	88261096	130013102
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87515716	126232097
Mapped(QC-failed)	0	0
% Mapped	99.1600	97.0900
Paired	88261096	130013102
Paired(QC-failed)	0	0
Read1	44130548	65006551
Read1(QC-failed)	0	0
Read2	44130548	65006551
Read2(QC-failed)	0	0
Properly Paired	81316073	109107434
Properly Paired(QC-failed)	0	0
% Properly Paired	92.1300	83.9200
With itself	87168708	124767100
With itself(QC-failed)	0	0
Singletons	347008	1464997
Singletons(QC-failed)	0	0
% Singleton	0.3900	1.1300
Diff. Chroms	4942561	11420887
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	38068211	48591962
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	532217	535380
Paired Opt. Dupes	3444	1721
% Dupes/100	0.0140	0.0110

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38066879	48585687
Distinct Read Pairs	37534679	48050759
One Read Pair	37021807	47543477
Two Read Pairs	495672	492610
NRF = Distinct/Total	0.9860	0.9890
PBC1 = OnePair/Distinct	0.9863	0.9894
PBC2 = OnePair/TwoPair	74.6901	96.5134

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	75071988	96113164
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75071988	96113164
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75071988	96113164
Paired(QC-failed)	0	0
Read1	37535994	48056582
Read1(QC-failed)	0	0
Read2	37535994	48056582
Read2(QC-failed)	0	0
Properly Paired	75071988	96113164
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75071988	96113164
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	197998
Np	0
N optimal	197998
N conservative	197998
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.	0.2035
Phantom Peak	55
Corr. Phantom Peak	0.1904
Argmin. Corr.	1500
Min. Corr.	0.1754
NSC	1.1602
RSC	1.8797

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	0.6243

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	0.1148
AUC	0.4953
CHANCE divergence	0.2410
Elbow Point	0.0000
JS Distance	0.8019
Synthetic AUC	0.5030
Synthetic Elbow Point	0.4126
Synthetic JS Distance	0.5402