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Report generated at 2020-06-06 01:08:45

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	85431646	121716226
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	77066074	120134777
Mapped(QC-failed)	0	0
% Mapped	90.2100	98.7000
Paired	85431646	121716226
Paired(QC-failed)	0	0
Read1	42715823	60858113
Read1(QC-failed)	0	0
Read2	42715823	60858113
Read2(QC-failed)	0	0
Properly Paired	74558318	118947303
Properly Paired(QC-failed)	0	0
% Properly Paired	87.2700	97.7300
With itself	75543409	119535099
With itself(QC-failed)	0	0
Singletons	1522665	599678
Singletons(QC-failed)	0	0
% Singleton	1.7800	0.4900
Diff. Chroms	185895	121425
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	28657250	52668443
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	16520937	2441741
Paired Opt. Dupes	8103	11372
% Dupes/100	0.5765	0.0464

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28654009	52600749
Distinct Read Pairs	12134815	50164652
One Read Pair	5325718	47837615
Two Read Pairs	2824806	2226928
NRF = Distinct/Total	0.4235	0.9537
PBC1 = OnePair/Distinct	0.4389	0.9536
PBC2 = OnePair/TwoPair	1.8853	21.4814

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	24272626	100453404
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	24272626	100453404
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	24272626	100453404
Paired(QC-failed)	0	0
Read1	12136313	50226702
Read1(QC-failed)	0	0
Read2	12136313	50226702
Read2(QC-failed)	0	0
Properly Paired	24272626	100453404
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	24272626	100453404
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	69572
Np	0
N optimal	69572
N conservative	69572
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.	180
Corr. Est. Fragment Len.	0.1656
Phantom Peak	50
Corr. Phantom Peak	0.1941
Argmin. Corr.	1500
Min. Corr.	0.1331
NSC	1.2444
RSC	0.5329

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	0.2310

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	0.1855
AUC	0.4917
CHANCE divergence	0.2619
Elbow Point	0.0000
JS Distance	0.6540
Synthetic AUC	0.5033
Synthetic Elbow Point	0.2531
Synthetic JS Distance	0.3789