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Report generated at 2021-03-22 01:00:22

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	76136108	98701132
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65992553	62974219
Mapped(QC-failed)	0	0
% Mapped	86.6800	63.8000
Paired	76136108	98701132
Paired(QC-failed)	0	0
Read1	38068054	49350566
Read1(QC-failed)	0	0
Read2	38068054	49350566
Read2(QC-failed)	0	0
Properly Paired	59220966	42858024
Properly Paired(QC-failed)	0	0
% Properly Paired	77.7800	43.4200
With itself	64860937	58789955
With itself(QC-failed)	0	0
Singletons	1131616	4184264
Singletons(QC-failed)	0	0
% Singleton	1.4900	4.2400
Diff. Chroms	2829308	5075489
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	26610350	18554885
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	511097	259126
Paired Opt. Dupes	2495	1094
% Dupes/100	0.0192	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26605651	18553556
Distinct Read Pairs	26094726	18294490
One Read Pair	25595307	18054489
Two Read Pairs	488979	229873
NRF = Distinct/Total	0.9808	0.9860
PBC1 = OnePair/Distinct	0.9809	0.9869
PBC2 = OnePair/TwoPair	52.3444	78.5411

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	52198506	36591518
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52198506	36591518
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52198506	36591518
Paired(QC-failed)	0	0
Read1	26099253	18295759
Read1(QC-failed)	0	0
Read2	26099253	18295759
Read2(QC-failed)	0	0
Properly Paired	52198506	36591518
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52198506	36591518
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	91137
Np	0
N optimal	91137
N conservative	91137
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.	150
Corr. Est. Fragment Len.	0.1791
Phantom Peak	50
Corr. Phantom Peak	0.1779
Argmin. Corr.	1500
Min. Corr.	0.1714
NSC	1.0450
RSC	1.1828

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	0.1804

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	0.2309
AUC	0.4956
CHANCE divergence	0.1383
Elbow Point	0.0000
JS Distance	0.6393
Synthetic AUC	0.5023
Synthetic Elbow Point	0.1124
Synthetic JS Distance	0.3513