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Report generated at 2020-12-04 21:34:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	70712892	334658014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	69652233	328702336
Mapped(QC-failed)	0	0
% Mapped	98.5000	98.2200
Paired	70712892	334658014
Paired(QC-failed)	0	0
Read1	35356446	167329007
Read1(QC-failed)	0	0
Read2	35356446	167329007
Read2(QC-failed)	0	0
Properly Paired	68925822	320102484
Properly Paired(QC-failed)	0	0
% Properly Paired	97.4700	95.6500
With itself	69232191	326658529
With itself(QC-failed)	0	0
Singletons	420042	2043807
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.6100
Diff. Chroms	141529	620372
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	30430601	141663705
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	434373	1830718
Paired Opt. Dupes	8059	10233
% Dupes/100	0.0143	0.0129

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30423315	141095473
Distinct Read Pairs	29989055	139340732
One Read Pair	29560212	137631421
Two Read Pairs	423501	1682298
NRF = Distinct/Total	0.9857	0.9876
PBC1 = OnePair/Distinct	0.9857	0.9877
PBC2 = OnePair/TwoPair	69.7996	81.8116

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	59992456	279665974
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59992456	279665974
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	59992456	279665974
Paired(QC-failed)	0	0
Read1	29996228	139832987
Read1(QC-failed)	0	0
Read2	29996228	139832987
Read2(QC-failed)	0	0
Properly Paired	59992456	279665974
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	59992456	279665974
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	126871
Np	0
N optimal	126871
N conservative	126871
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.	180
Corr. Est. Fragment Len.	0.2102
Phantom Peak	50
Corr. Phantom Peak	0.2084
Argmin. Corr.	1500
Min. Corr.	0.1852
NSC	1.1352
RSC	1.0810

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	0.3621

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	0.1903
AUC	0.4947
CHANCE divergence	0.1500
Elbow Point	0.0000
JS Distance	0.7248
Synthetic AUC	0.4989
Synthetic Elbow Point	0.3503
Synthetic JS Distance	0.4261