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Report generated at 2021-10-10 06:22:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	140387230	135940090
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	137797644	134333469
Mapped(QC-failed)	0	0
% Mapped	98.1600	98.8200
Paired	140387230	135940090
Paired(QC-failed)	0	0
Read1	70193615	67970045
Read1(QC-failed)	0	0
Read2	70193615	67970045
Read2(QC-failed)	0	0
Properly Paired	136739181	131959627
Properly Paired(QC-failed)	0	0
% Properly Paired	97.4000	97.0700
With itself	137076741	133529071
With itself(QC-failed)	0	0
Singletons	720903	804398
Singletons(QC-failed)	0	0
% Singleton	0.5100	0.5900
Diff. Chroms	116045	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	59961230	55193949
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11877374	3483873
Paired Opt. Dupes	45798	49939
% Dupes/100	0.1981	0.0631

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	59960145	55175675
Distinct Read Pairs	48082980	51692963
One Read Pair	38207274	48296105
Two Read Pairs	8176825	3315273
NRF = Distinct/Total	0.8019	0.9369
PBC1 = OnePair/Distinct	0.7946	0.9343
PBC2 = OnePair/TwoPair	4.6726	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	96167712	103420152
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96167712	103420152
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	96167712	103420152
Paired(QC-failed)	0	0
Read1	48083856	51710076
Read1(QC-failed)	0	0
Read2	48083856	51710076
Read2(QC-failed)	0	0
Properly Paired	96167712	103420152
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	96167712	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	126029
Np	0
N optimal	126029
N conservative	126029
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.	195
Corr. Est. Fragment Len.	0.2319
Phantom Peak	50
Corr. Phantom Peak	0.2254
Argmin. Corr.	1500
Min. Corr.	0.1860
NSC	1.2468
RSC	1.1647

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	0.5119

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	0.1516
AUC	0.4949
CHANCE divergence	0.1278
Elbow Point	0.0000
JS Distance	0.8091
Synthetic AUC	0.4954
Synthetic Elbow Point	0.4149
Synthetic JS Distance	0.5090