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Report generated at 2020-07-15 22:47:01

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	167434402	168466658
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	150749171	164624745
Mapped(QC-failed)	0	0
% Mapped	90.0300	97.7200
Paired	167434402	168466658
Paired(QC-failed)	0	0
Read1	83717201	84233329
Read1(QC-failed)	0	0
Read2	83717201	84233329
Read2(QC-failed)	0	0
Properly Paired	145543393	162184899
Properly Paired(QC-failed)	0	0
% Properly Paired	86.9300	96.2700
With itself	148079577	163825228
With itself(QC-failed)	0	0
Singletons	2669594	799517
Singletons(QC-failed)	0	0
% Singleton	1.5900	0.4700
Diff. Chroms	758566	775348
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	53272487	70866487
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	378814	312564
Paired Opt. Dupes	9982	1254
% Dupes/100	0.0071	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	53266427	70787609
Distinct Read Pairs	52887657	70476699
One Read Pair	52517812	70167382
Two Read Pairs	362257	307768
NRF = Distinct/Total	0.9929	0.9956
PBC1 = OnePair/Distinct	0.9930	0.9956
PBC2 = OnePair/TwoPair	144.9739	227.9879

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	105787346	141107846
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105787346	141107846
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	105787346	141107846
Paired(QC-failed)	0	0
Read1	52893673	70553923
Read1(QC-failed)	0	0
Read2	52893673	70553923
Read2(QC-failed)	0	0
Properly Paired	105787346	141107846
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	105787346	141107846
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	232643
Np	0
N optimal	232643
N conservative	232643
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.	115
Corr. Est. Fragment Len.	0.2023
Phantom Peak	50
Corr. Phantom Peak	0.2544
Argmin. Corr.	1500
Min. Corr.	0.1876
NSC	1.0780
RSC	0.2191

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	0.2311

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	0.2517
AUC	0.4960
CHANCE divergence	0.1026
Elbow Point	0.0000
JS Distance	0.6446
Synthetic AUC	0.4963
Synthetic Elbow Point	0.1709
Synthetic JS Distance	0.3312