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Report generated at 2021-10-21 03:26:36

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	118542584	135940090
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117613892	134333469
Mapped(QC-failed)	0	0
% Mapped	99.2200	98.8200
Paired	118542584	135940090
Paired(QC-failed)	0	0
Read1	59271292	67970045
Read1(QC-failed)	0	0
Read2	59271292	67970045
Read2(QC-failed)	0	0
Properly Paired	116283631	131959627
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0900	97.0700
With itself	117077109	133529071
With itself(QC-failed)	0	0
Singletons	536783	804398
Singletons(QC-failed)	0	0
% Singleton	0.4500	0.5900
Diff. Chroms	494749	898860
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	49253450	55193949
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3291382	3483873
Paired Opt. Dupes	49309	49939
% Dupes/100	0.0668	0.0631

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49253317	55175675
Distinct Read Pairs	45961946	51692963
One Read Pair	42787417	48296105
Two Read Pairs	3062830	3315273
NRF = Distinct/Total	0.9332	0.9369
PBC1 = OnePair/Distinct	0.9309	0.9343
PBC2 = OnePair/TwoPair	13.9699	14.5678

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	91924136	103420152
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91924136	103420152
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	91924136	103420152
Paired(QC-failed)	0	0
Read1	45962068	51710076
Read1(QC-failed)	0	0
Read2	45962068	51710076
Read2(QC-failed)	0	0
Properly Paired	91924136	103420152
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	91924136	103420152
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	115048
Np	0
N optimal	115048
N conservative	115048
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.	210
Corr. Est. Fragment Len.	0.2005
Phantom Peak	50
Corr. Phantom Peak	0.2017
Argmin. Corr.	1500
Min. Corr.	0.1957
NSC	1.0244
RSC	0.7937

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	0.6457

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	0.1177
AUC	0.4948
CHANCE divergence	0.1896
Elbow Point	0.0000
JS Distance	0.8043
Synthetic AUC	0.5035
Synthetic Elbow Point	0.4462
Synthetic JS Distance	0.5504