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Report generated at 2022-01-07 01:24:26

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	207398620	201652566
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	205395634	198032065
Mapped(QC-failed)	0	0
% Mapped	99.0300	98.2000
Paired	207398620	201652566
Paired(QC-failed)	0	0
Read1	103699310	100826283
Read1(QC-failed)	0	0
Read2	103699310	100826283
Read2(QC-failed)	0	0
Properly Paired	187141236	194936556
Properly Paired(QC-failed)	0	0
% Properly Paired	90.2300	96.6700
With itself	204213834	196867125
With itself(QC-failed)	0	0
Singletons	1181800	1164940
Singletons(QC-failed)	0	0
% Singleton	0.5700	0.5800
Diff. Chroms	272305	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	85180386	84633399
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4774374	1125235
Paired Opt. Dupes	1470	1306
% Dupes/100	0.0561	0.0133

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	85168807	84626173
Distinct Read Pairs	80395885	83501515
One Read Pair	76007277	82459535
Two Read Pairs	4067805	999176
NRF = Distinct/Total	0.9440	0.9867
PBC1 = OnePair/Distinct	0.9454	0.9875
PBC2 = OnePair/TwoPair	18.6851	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	160812024	167016328
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	160812024	167016328
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	160812024	167016328
Paired(QC-failed)	0	0
Read1	80406012	83508164
Read1(QC-failed)	0	0
Read2	80406012	83508164
Read2(QC-failed)	0	0
Properly Paired	160812024	167016328
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	160812024	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	249966
Np	0
N optimal	249966
N conservative	249966
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.	0.1865
Phantom Peak	45
Corr. Phantom Peak	0.1786
Argmin. Corr.	1500
Min. Corr.	0.1743
NSC	1.0700
RSC	2.8079

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	0.3895

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	0.1982
AUC	0.4968
CHANCE divergence	0.1384
Elbow Point	0.0000
JS Distance	0.6691
Synthetic AUC	0.5032
Synthetic Elbow Point	0.2384
Synthetic JS Distance	0.4116