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Report generated at 2020-06-05 18:10:27

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	137901364	65794820
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	133782950	63417692
Mapped(QC-failed)	0	0
% Mapped	97.0100	96.3900
Paired	137901364	65794820
Paired(QC-failed)	0	0
Read1	68950682	32897410
Read1(QC-failed)	0	0
Read2	68950682	32897410
Read2(QC-failed)	0	0
Properly Paired	131482375	61746812
Properly Paired(QC-failed)	0	0
% Properly Paired	95.3500	93.8500
With itself	131898042	61970109
With itself(QC-failed)	0	0
Singletons	1884908	1447583
Singletons(QC-failed)	0	0
% Singleton	1.3700	2.2000
Diff. Chroms	92720	55379
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	57356883	26833523
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8904866	435866
Paired Opt. Dupes	4121	1445
% Dupes/100	0.1553	0.0162

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	57356061	26817652
Distinct Read Pairs	48451328	26382149
One Read Pair	40713689	25952967
Two Read Pairs	6705042	422975
NRF = Distinct/Total	0.8447	0.9838
PBC1 = OnePair/Distinct	0.8403	0.9837
PBC2 = OnePair/TwoPair	6.0721	61.3582

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	96904034	52795314
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96904034	52795314
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	96904034	52795314
Paired(QC-failed)	0	0
Read1	48452017	26397657
Read1(QC-failed)	0	0
Read2	48452017	26397657
Read2(QC-failed)	0	0
Properly Paired	96904034	52795314
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	96904034	52795314
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	97538
Np	0
N optimal	97538
N conservative	97538
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.	185
Corr. Est. Fragment Len.	0.1730
Phantom Peak	50
Corr. Phantom Peak	0.1845
Argmin. Corr.	1500
Min. Corr.	0.1674
NSC	1.0334
RSC	0.3274

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	0.1038

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	0.3069
AUC	0.4959
CHANCE divergence	0.0987
Elbow Point	0.0000
JS Distance	0.5705
Synthetic AUC	0.4993
Synthetic Elbow Point	0.0815
Synthetic JS Distance	0.2417