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Report generated at 2020-07-15 00:37:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	88217614	155229270
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85921355	150942743
Mapped(QC-failed)	0	0
% Mapped	97.4000	97.2400
Paired	88217614	155229270
Paired(QC-failed)	0	0
Read1	44108807	77614635
Read1(QC-failed)	0	0
Read2	44108807	77614635
Read2(QC-failed)	0	0
Properly Paired	84667588	148607764
Properly Paired(QC-failed)	0	0
% Properly Paired	95.9800	95.7300
With itself	85525690	150154922
With itself(QC-failed)	0	0
Singletons	395665	787821
Singletons(QC-failed)	0	0
% Singleton	0.4500	0.5100
Diff. Chroms	532275	787266
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	38337809	64735106
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	155311	274206
Paired Opt. Dupes	1325	1163
% Dupes/100	0.0041	0.0042

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38332626	64655208
Distinct Read Pairs	38177335	64382549
One Read Pair	38022590	64112121
Two Read Pairs	154203	268358
NRF = Distinct/Total	0.9959	0.9958
PBC1 = OnePair/Distinct	0.9959	0.9958
PBC2 = OnePair/TwoPair	246.5749	238.9052

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	76364996	128921800
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76364996	128921800
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76364996	128921800
Paired(QC-failed)	0	0
Read1	38182498	64460900
Read1(QC-failed)	0	0
Read2	38182498	64460900
Read2(QC-failed)	0	0
Properly Paired	76364996	128921800
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76364996	128921800
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	183001
Np	0
N optimal	183001
N conservative	183001
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.	140
Corr. Est. Fragment Len.	0.1839
Phantom Peak	50
Corr. Phantom Peak	0.1921
Argmin. Corr.	1500
Min. Corr.	0.1756
NSC	1.0472
RSC	0.5024

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	0.2333

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	0.2329
AUC	0.4953
CHANCE divergence	0.1199
Elbow Point	0.0000
JS Distance	0.6575
Synthetic AUC	0.5074
Synthetic Elbow Point	0.1959
Synthetic JS Distance	0.3507