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Report generated at 2021-03-21 23:40:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	69644746	98701132
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63378819	62974219
Mapped(QC-failed)	0	0
% Mapped	91.0000	63.8000
Paired	69644746	98701132
Paired(QC-failed)	0	0
Read1	34822373	49350566
Read1(QC-failed)	0	0
Read2	34822373	49350566
Read2(QC-failed)	0	0
Properly Paired	58475049	42858024
Properly Paired(QC-failed)	0	0
% Properly Paired	83.9600	43.4200
With itself	62680650	58789955
With itself(QC-failed)	0	0
Singletons	698169	4184264
Singletons(QC-failed)	0	0
% Singleton	1.0000	4.2400
Diff. Chroms	1952144	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	26715999	18554885
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	479048	259126
Paired Opt. Dupes	1901	1094
% Dupes/100	0.0179	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26708737	18553556
Distinct Read Pairs	26229985	18294490
One Read Pair	25761112	18054489
Two Read Pairs	459399	229873
NRF = Distinct/Total	0.9821	0.9860
PBC1 = OnePair/Distinct	0.9821	0.9869
PBC2 = OnePair/TwoPair	56.0757	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	52473902	36591518
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52473902	36591518
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52473902	36591518
Paired(QC-failed)	0	0
Read1	26236951	18295759
Read1(QC-failed)	0	0
Read2	26236951	18295759
Read2(QC-failed)	0	0
Properly Paired	52473902	36591518
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52473902	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	191359
Np	0
N optimal	191359
N conservative	191359
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.	160
Corr. Est. Fragment Len.	0.1999
Phantom Peak	55
Corr. Phantom Peak	0.1890
Argmin. Corr.	1500
Min. Corr.	0.1873
NSC	1.0674
RSC	7.4319

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	0.5991

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	0.1063
AUC	0.4956
CHANCE divergence	0.3108
Elbow Point	0.0000
JS Distance	0.8045
Synthetic AUC	0.5078
Synthetic Elbow Point	0.3109
Synthetic JS Distance	0.5364