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Report generated at 2020-05-22 13:07:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63992852	101616908
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60381698	98299386
Mapped(QC-failed)	0	0
% Mapped	94.3600	96.7400
Paired	63992852	101616908
Paired(QC-failed)	0	0
Read1	31996426	50808454
Read1(QC-failed)	0	0
Read2	31996426	50808454
Read2(QC-failed)	0	0
Properly Paired	59559184	95630320
Properly Paired(QC-failed)	0	0
% Properly Paired	93.0700	94.1100
With itself	60101206	97482566
With itself(QC-failed)	0	0
Singletons	280492	816820
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.8000
Diff. Chroms	323268	1199069
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	27075060	41555789
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	98937	219396
Paired Opt. Dupes	601	598
% Dupes/100	0.0037	0.0053

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27072793	41491091
Distinct Read Pairs	26973863	41273018
One Read Pair	26875243	41056255
Two Read Pairs	98310	215467
NRF = Distinct/Total	0.9963	0.9947
PBC1 = OnePair/Distinct	0.9963	0.9947
PBC2 = OnePair/TwoPair	273.3724	190.5454

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	53952246	82672786
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53952246	82672786
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	53952246	82672786
Paired(QC-failed)	0	0
Read1	26976123	41336393
Read1(QC-failed)	0	0
Read2	26976123	41336393
Read2(QC-failed)	0	0
Properly Paired	53952246	82672786
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	53952246	82672786
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	85067
Np	0
N optimal	85067
N conservative	85067
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.	165
Corr. Est. Fragment Len.	0.1909
Phantom Peak	50
Corr. Phantom Peak	0.1953
Argmin. Corr.	1500
Min. Corr.	0.1787
NSC	1.0688
RSC	0.7396

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	0.2102

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	0.2188
AUC	0.4945
CHANCE divergence	0.1336
Elbow Point	0.0000
JS Distance	0.6773
Synthetic AUC	0.5029
Synthetic Elbow Point	0.1527
Synthetic JS Distance	0.3731