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Report generated at 2020-11-26 10:09:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	110027028	148269018
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108403685	143500908
Mapped(QC-failed)	0	0
% Mapped	98.5200	96.7800
Paired	110027028	148269018
Paired(QC-failed)	0	0
Read1	55013514	74134509
Read1(QC-failed)	0	0
Read2	55013514	74134509
Read2(QC-failed)	0	0
Properly Paired	107047549	140225987
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2900	94.5800
With itself	107945418	141622671
With itself(QC-failed)	0	0
Singletons	458267	1878237
Singletons(QC-failed)	0	0
% Singleton	0.4200	1.2700
Diff. Chroms	495824	652729
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	47482922	59090669
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	765946	523701
Paired Opt. Dupes	6085	14446
% Dupes/100	0.0161	0.0089

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47444858	57674075
Distinct Read Pairs	46679802	57472830
One Read Pair	45925450	57272993
Two Read Pairs	743786	198503
NRF = Distinct/Total	0.9839	0.9965
PBC1 = OnePair/Distinct	0.9838	0.9965
PBC2 = OnePair/TwoPair	61.7455	288.5246

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	93433952	117133936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	93433952	117133936
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	93433952	117133936
Paired(QC-failed)	0	0
Read1	46716976	58566968
Read1(QC-failed)	0	0
Read2	46716976	58566968
Read2(QC-failed)	0	0
Properly Paired	93433952	117133936
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	93433952	117133936
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	85130
Np	0
N optimal	85130
N conservative	85130
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.	185
Corr. Est. Fragment Len.	0.1879
Phantom Peak	50
Corr. Phantom Peak	0.1935
Argmin. Corr.	1500
Min. Corr.	0.1768
NSC	1.0629
RSC	0.6661

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	0.1919

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	0.2648
AUC	0.4958
CHANCE divergence	0.1012
Elbow Point	0.0000
JS Distance	0.6310
Synthetic AUC	0.5031
Synthetic Elbow Point	0.2125
Synthetic JS Distance	0.3191