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Report generated at 2020-06-05 11:23:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	59286720	94272842
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57064940	92659557
Mapped(QC-failed)	0	0
% Mapped	96.2500	98.2900
Paired	59286720	94272842
Paired(QC-failed)	0	0
Read1	29643360	47136421
Read1(QC-failed)	0	0
Read2	29643360	47136421
Read2(QC-failed)	0	0
Properly Paired	55445563	91574742
Properly Paired(QC-failed)	0	0
% Properly Paired	93.5200	97.1400
With itself	55625479	92304558
With itself(QC-failed)	0	0
Singletons	1439461	354999
Singletons(QC-failed)	0	0
% Singleton	2.4300	0.3800
Diff. Chroms	35396	370286
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	24078487	40575988
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10436862	1257392
Paired Opt. Dupes	1463	3763
% Dupes/100	0.4335	0.0310

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24056289	40180957
Distinct Read Pairs	13627327	38989114
One Read Pair	8454433	37836528
Two Read Pairs	2644560	1116568
NRF = Distinct/Total	0.5665	0.9703
PBC1 = OnePair/Distinct	0.6204	0.9704
PBC2 = OnePair/TwoPair	3.1969	33.8865

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	27283250	78637192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	27283250	78637192
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	27283250	78637192
Paired(QC-failed)	0	0
Read1	13641625	39318596
Read1(QC-failed)	0	0
Read2	13641625	39318596
Read2(QC-failed)	0	0
Properly Paired	27283250	78637192
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	27283250	78637192
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	45462
Np	0
N optimal	45462
N conservative	45462
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.	155
Corr. Est. Fragment Len.	0.1440
Phantom Peak	50
Corr. Phantom Peak	0.1475
Argmin. Corr.	1500
Min. Corr.	0.1220
NSC	1.1808
RSC	0.8637

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	0.0808

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	0.2399
AUC	0.4922
CHANCE divergence	0.2114
Elbow Point	0.0000
JS Distance	0.5942
Synthetic AUC	0.5129
Synthetic Elbow Point	0.1506
Synthetic JS Distance	0.2898