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Report generated at 2020-06-06 03:26:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120324612	94272842
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115020492	92659557
Mapped(QC-failed)	0	0
% Mapped	95.5900	98.2900
Paired	120324612	94272842
Paired(QC-failed)	0	0
Read1	60162306	47136421
Read1(QC-failed)	0	0
Read2	60162306	47136421
Read2(QC-failed)	0	0
Properly Paired	113365198	91574742
Properly Paired(QC-failed)	0	0
% Properly Paired	94.2200	97.1400
With itself	114031053	92304558
With itself(QC-failed)	0	0
Singletons	989439	354999
Singletons(QC-failed)	0	0
% Singleton	0.8200	0.3800
Diff. Chroms	117964	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	46234172	40575988
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	23457228	1257392
Paired Opt. Dupes	3837	3763
% Dupes/100	0.5074	0.0310

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46188644	40180957
Distinct Read Pairs	22754341	38989114
One Read Pair	13667185	37836528
Two Read Pairs	4116506	1116568
NRF = Distinct/Total	0.4926	0.9703
PBC1 = OnePair/Distinct	0.6006	0.9704
PBC2 = OnePair/TwoPair	3.3201	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	45553888	78637192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45553888	78637192
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45553888	78637192
Paired(QC-failed)	0	0
Read1	22776944	39318596
Read1(QC-failed)	0	0
Read2	22776944	39318596
Read2(QC-failed)	0	0
Properly Paired	45553888	78637192
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45553888	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	43520
Np	0
N optimal	43520
N conservative	43520
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.	145
Corr. Est. Fragment Len.	0.1489
Phantom Peak	50
Corr. Phantom Peak	0.1787
Argmin. Corr.	1500
Min. Corr.	0.1334
NSC	1.1160
RSC	0.3422

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	0.0255

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	0.2842
AUC	0.4940
CHANCE divergence	0.1378
Elbow Point	0.0000
JS Distance	0.5429
Synthetic AUC	0.5034
Synthetic Elbow Point	0.0878
Synthetic JS Distance	0.2524