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Report generated at 2020-05-04 06:59:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	144798752	163903192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103465281	160420879
Mapped(QC-failed)	0	0
% Mapped	71.4500	97.8800
Paired	144798752	163903192
Paired(QC-failed)	0	0
Read1	72399376	81951596
Read1(QC-failed)	0	0
Read2	72399376	81951596
Read2(QC-failed)	0	0
Properly Paired	101548560	158734975
Properly Paired(QC-failed)	0	0
% Properly Paired	70.1300	96.8500
With itself	102210663	159739476
With itself(QC-failed)	0	0
Singletons	1254618	681403
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.4200
Diff. Chroms	244537	350799
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	44851177	69550649
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	357579	430368
Paired Opt. Dupes	1940	2814
% Dupes/100	0.0080	0.0062

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44845416	69493062
Distinct Read Pairs	44487900	69063958
One Read Pair	44133519	68639549
Two Read Pairs	351354	420276
NRF = Distinct/Total	0.9920	0.9938
PBC1 = OnePair/Distinct	0.9920	0.9939
PBC2 = OnePair/TwoPair	125.6098	163.3202

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	88987196	138240562
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88987196	138240562
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	88987196	138240562
Paired(QC-failed)	0	0
Read1	44493598	69120281
Read1(QC-failed)	0	0
Read2	44493598	69120281
Read2(QC-failed)	0	0
Properly Paired	88987196	138240562
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	88987196	138240562
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	221322
Np	0
N optimal	221322
N conservative	221322
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.	120
Corr. Est. Fragment Len.	0.1891
Phantom Peak	50
Corr. Phantom Peak	0.2238
Argmin. Corr.	1500
Min. Corr.	0.1741
NSC	1.0863
RSC	0.3022

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	0.2667

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	0.2076
AUC	0.4957
CHANCE divergence	0.1455
Elbow Point	0.0000
JS Distance	0.6717
Synthetic AUC	0.5019
Synthetic Elbow Point	0.1787
Synthetic JS Distance	0.3881