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Report generated at 2022-01-15 07:54:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	32592726	98701132
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	32057806	96181840
Mapped(QC-failed)	0	0
% Mapped	98.3600	97.4500
Paired	32592726	98701132
Paired(QC-failed)	0	0
Read1	16296363	49350566
Read1(QC-failed)	0	0
Read2	16296363	49350566
Read2(QC-failed)	0	0
Properly Paired	30572380	77055364
Properly Paired(QC-failed)	0	0
% Properly Paired	93.8000	78.0700
With itself	31762535	94971565
With itself(QC-failed)	0	0
Singletons	295271	1210275
Singletons(QC-failed)	0	0
% Singleton	0.9100	1.2300
Diff. Chroms	994797	14544721
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	14108646	34047307
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	467503	359515
Paired Opt. Dupes	1606	1894
% Dupes/100	0.0331	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	14104238	34044272
Distinct Read Pairs	13636875	33684905
One Read Pair	13209650	33341128
Two Read Pairs	397226	333429
NRF = Distinct/Total	0.9669	0.9894
PBC1 = OnePair/Distinct	0.9687	0.9898
PBC2 = OnePair/TwoPair	33.2547	99.9947

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	27282286	67375584
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	27282286	67375584
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	27282286	67375584
Paired(QC-failed)	0	0
Read1	13641143	33687792
Read1(QC-failed)	0	0
Read2	13641143	33687792
Read2(QC-failed)	0	0
Properly Paired	27282286	67375584
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	27282286	67375584
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	63327
Np	0
N optimal	63327
N conservative	63327
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.	160
Corr. Est. Fragment Len.	0.2865
Phantom Peak	55
Corr. Phantom Peak	0.2222
Argmin. Corr.	1500
Min. Corr.	0.1606
NSC	1.7841
RSC	2.0440

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	0.6740

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	0.0676
AUC	0.4922
CHANCE divergence	0.4296
Elbow Point	0.0000
JS Distance	0.8982
Synthetic AUC	0.4932
Synthetic Elbow Point	0.5192
Synthetic JS Distance	0.6222