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Report generated at 2020-07-15 10:30:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	140318822	161541774
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	124455748	157457809
Mapped(QC-failed)	0	0
% Mapped	88.6900	97.4700
Paired	140318822	161541774
Paired(QC-failed)	0	0
Read1	70159411	80770887
Read1(QC-failed)	0	0
Read2	70159411	80770887
Read2(QC-failed)	0	0
Properly Paired	122200437	154923170
Properly Paired(QC-failed)	0	0
% Properly Paired	87.0900	95.9000
With itself	123307777	156706856
With itself(QC-failed)	0	0
Singletons	1147971	750953
Singletons(QC-failed)	0	0
% Singleton	0.8200	0.4600
Diff. Chroms	537729	1033935
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	52404744	67677947
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	282869	255439
Paired Opt. Dupes	2507	1182
% Dupes/100	0.0054	0.0038

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52400444	67623047
Distinct Read Pairs	52117601	67368479
One Read Pair	51836374	67115243
Two Read Pairs	279626	251987
NRF = Distinct/Total	0.9946	0.9962
PBC1 = OnePair/Distinct	0.9946	0.9962
PBC2 = OnePair/TwoPair	185.3775	266.3441

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	104243750	134845016
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104243750	134845016
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	104243750	134845016
Paired(QC-failed)	0	0
Read1	52121875	67422508
Read1(QC-failed)	0	0
Read2	52121875	67422508
Read2(QC-failed)	0	0
Properly Paired	104243750	134845016
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	104243750	134845016
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	97607
Np	0
N optimal	97607
N conservative	97607
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.	0.1823
Phantom Peak	50
Corr. Phantom Peak	0.2111
Argmin. Corr.	1500
Min. Corr.	0.1733
NSC	1.0519
RSC	0.2376

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	0.0575

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	0.2999
AUC	0.4960
CHANCE divergence	0.1002
Elbow Point	0.0000
JS Distance	0.5663
Synthetic AUC	0.5072
Synthetic Elbow Point	0.0778
Synthetic JS Distance	0.2476