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Report generated at 2022-09-02 22:50:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	167320282	50889240
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	160645879	50058651
Mapped(QC-failed)	0	0
% Mapped	96.0100	98.3700
Paired	167320282	50889240
Paired(QC-failed)	0	0
Read1	83660141	25444620
Read1(QC-failed)	0	0
Read2	83660141	25444620
Read2(QC-failed)	0	0
Properly Paired	158777889	49717706
Properly Paired(QC-failed)	0	0
% Properly Paired	94.8900	97.7000
With itself	159956928	49906072
With itself(QC-failed)	0	0
Singletons	688951	152579
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.3000
Diff. Chroms	257665	67298
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	70607430	22060886
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	978194	95014
Paired Opt. Dupes	8575	6064
% Dupes/100	0.0139	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	70604078	22024154
Distinct Read Pairs	69625930	21929940
One Read Pair	68662206	21836362
Two Read Pairs	950087	93000
NRF = Distinct/Total	0.9861	0.9957
PBC1 = OnePair/Distinct	0.9862	0.9957
PBC2 = OnePair/TwoPair	72.2694	234.7996

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	139258472	43931744
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	139258472	43931744
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	139258472	43931744
Paired(QC-failed)	0	0
Read1	69629236	21965872
Read1(QC-failed)	0	0
Read2	69629236	21965872
Read2(QC-failed)	0	0
Properly Paired	139258472	43931744
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	139258472	43931744
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	60392
Np	0
N optimal	60392
N conservative	60392
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.	125
Corr. Est. Fragment Len.	0.1833
Phantom Peak	50
Corr. Phantom Peak	0.2012
Argmin. Corr.	1500
Min. Corr.	0.1752
NSC	1.0466
RSC	0.3131

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	0.0478

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	0.2930
AUC	0.4966
CHANCE divergence	0.0999
Elbow Point	0.0000
JS Distance	0.5980
Synthetic AUC	0.5013
Synthetic Elbow Point	0.0644
Synthetic JS Distance	0.2635