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Report generated at 2021-07-07 22:46:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	97188966	148600262
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95437213	144098222
Mapped(QC-failed)	0	0
% Mapped	98.2000	96.9700
Paired	97188966	148600262
Paired(QC-failed)	0	0
Read1	48594483	74300131
Read1(QC-failed)	0	0
Read2	48594483	74300131
Read2(QC-failed)	0	0
Properly Paired	88471372	124201504
Properly Paired(QC-failed)	0	0
% Properly Paired	91.0300	83.5800
With itself	94732481	142351740
With itself(QC-failed)	0	0
Singletons	704732	1746482
Singletons(QC-failed)	0	0
% Singleton	0.7300	1.1800
Diff. Chroms	4670765	13088864
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	39392551	55069462
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	354246	517761
Paired Opt. Dupes	1266	1468
% Dupes/100	0.0090	0.0094

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39369247	55053291
Distinct Read Pairs	39017404	54537877
One Read Pair	38673461	54050644
Two Read Pairs	338887	474902
NRF = Distinct/Total	0.9911	0.9906
PBC1 = OnePair/Distinct	0.9912	0.9911
PBC2 = OnePair/TwoPair	114.1190	113.8143

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	78076610	109103402
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78076610	109103402
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78076610	109103402
Paired(QC-failed)	0	0
Read1	39038305	54551701
Read1(QC-failed)	0	0
Read2	39038305	54551701
Read2(QC-failed)	0	0
Properly Paired	78076610	109103402
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78076610	109103402
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	203505
Np	0
N optimal	203505
N conservative	203505
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.	-10
Corr. Est. Fragment Len.	0.1805
Phantom Peak	50
Corr. Phantom Peak	0.1831
Argmin. Corr.	1500
Min. Corr.	0.1742
NSC	1.0359
RSC	0.7040

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	0.3954

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	0.1966
AUC	0.4954
CHANCE divergence	0.1376
Elbow Point	0.0000
JS Distance	0.6945
Synthetic AUC	0.5020
Synthetic Elbow Point	0.2597
Synthetic JS Distance	0.4072