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Report generated at 2022-01-06 11:15:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104998134	201652566
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102645718	198032065
Mapped(QC-failed)	0	0
% Mapped	97.7600	98.2000
Paired	104998134	201652566
Paired(QC-failed)	0	0
Read1	52499067	100826283
Read1(QC-failed)	0	0
Read2	52499067	100826283
Read2(QC-failed)	0	0
Properly Paired	101090649	194936556
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2800	96.6700
With itself	102073195	196867125
With itself(QC-failed)	0	0
Singletons	572523	1164940
Singletons(QC-failed)	0	0
% Singleton	0.5500	0.5800
Diff. Chroms	43504	328067
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	46350168	84633399
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7400327	1125235
Paired Opt. Dupes	2850	1306
% Dupes/100	0.1597	0.0133

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46335146	84626173
Distinct Read Pairs	38937193	83501515
One Read Pair	32822353	82459535
Two Read Pairs	5216141	999176
NRF = Distinct/Total	0.8403	0.9867
PBC1 = OnePair/Distinct	0.8430	0.9875
PBC2 = OnePair/TwoPair	6.2925	82.5275

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	77899682	167016328
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	77899682	167016328
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	77899682	167016328
Paired(QC-failed)	0	0
Read1	38949841	83508164
Read1(QC-failed)	0	0
Read2	38949841	83508164
Read2(QC-failed)	0	0
Properly Paired	77899682	167016328
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	77899682	167016328
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	51370
Np	0
N optimal	51370
N conservative	51370
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.	0.2769
Phantom Peak	55
Corr. Phantom Peak	0.2101
Argmin. Corr.	1500
Min. Corr.	0.1742
NSC	1.5896
RSC	2.8623

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	0.4129

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	0.1819
AUC	0.4954
CHANCE divergence	0.1155
Elbow Point	0.0000
JS Distance	0.8165
Synthetic AUC	0.4969
Synthetic Elbow Point	0.3972
Synthetic JS Distance	0.4863