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Report generated at 2021-02-06 05:52:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	112245746	114964496
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108823651	113057292
Mapped(QC-failed)	0	0
% Mapped	96.9500	98.3400
Paired	112245746	114964496
Paired(QC-failed)	0	0
Read1	56122873	57482248
Read1(QC-failed)	0	0
Read2	56122873	57482248
Read2(QC-failed)	0	0
Properly Paired	105734825	110989369
Properly Paired(QC-failed)	0	0
% Properly Paired	94.2000	96.5400
With itself	107772124	112354296
With itself(QC-failed)	0	0
Singletons	1051527	702996
Singletons(QC-failed)	0	0
% Singleton	0.9400	0.6100
Diff. Chroms	171206	166080
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	40615191	48236755
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	488154	258071
Paired Opt. Dupes	21192	15943
% Dupes/100	0.0120	0.0053

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40592629	48217442
Distinct Read Pairs	40105321	47960279
One Read Pair	39683778	47714915
Two Read Pairs	402654	240532
NRF = Distinct/Total	0.9880	0.9947
PBC1 = OnePair/Distinct	0.9895	0.9949
PBC2 = OnePair/TwoPair	98.5555	198.3724

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	80254074	95957368
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80254074	95957368
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	80254074	95957368
Paired(QC-failed)	0	0
Read1	40127037	47978684
Read1(QC-failed)	0	0
Read2	40127037	47978684
Read2(QC-failed)	0	0
Properly Paired	80254074	95957368
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	80254074	95957368
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	226684
Np	0
N optimal	226684
N conservative	226684
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.	0.1889
Phantom Peak	50
Corr. Phantom Peak	0.2077
Argmin. Corr.	1500
Min. Corr.	0.1771
NSC	1.0663
RSC	0.3841

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	0.2994

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	0.2228
AUC	0.4953
CHANCE divergence	0.1171
Elbow Point	0.0000
JS Distance	0.6857
Synthetic AUC	0.5033
Synthetic Elbow Point	0.1755
Synthetic JS Distance	0.3688