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Report generated at 2020-05-21 02:58:07

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	136902576	163903192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	107467075	160420879
Mapped(QC-failed)	0	0
% Mapped	78.5000	97.8800
Paired	136902576	163903192
Paired(QC-failed)	0	0
Read1	68451288	81951596
Read1(QC-failed)	0	0
Read2	68451288	81951596
Read2(QC-failed)	0	0
Properly Paired	105899068	158734975
Properly Paired(QC-failed)	0	0
% Properly Paired	77.3500	96.8500
With itself	106517144	159739476
With itself(QC-failed)	0	0
Singletons	949931	681403
Singletons(QC-failed)	0	0
% Singleton	0.6900	0.4200
Diff. Chroms	237569	350799
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	47876852	69550649
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	321204	430368
Paired Opt. Dupes	1949	2814
% Dupes/100	0.0067	0.0062

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47871917	69493062
Distinct Read Pairs	47550752	69063958
One Read Pair	47231662	68639549
Two Read Pairs	317047	420276
NRF = Distinct/Total	0.9933	0.9938
PBC1 = OnePair/Distinct	0.9933	0.9939
PBC2 = OnePair/TwoPair	148.9737	163.3202

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	95111296	138240562
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95111296	138240562
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	95111296	138240562
Paired(QC-failed)	0	0
Read1	47555648	69120281
Read1(QC-failed)	0	0
Read2	47555648	69120281
Read2(QC-failed)	0	0
Properly Paired	95111296	138240562
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	95111296	138240562
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	219927
Np	0
N optimal	219927
N conservative	219927
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.	115
Corr. Est. Fragment Len.	0.1844
Phantom Peak	50
Corr. Phantom Peak	0.2064
Argmin. Corr.	1500
Min. Corr.	0.1718
NSC	1.0735
RSC	0.3646

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	0.2301

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	0.2152
AUC	0.4958
CHANCE divergence	0.1413
Elbow Point	0.0000
JS Distance	0.6557
Synthetic AUC	0.5059
Synthetic Elbow Point	0.1576
Synthetic JS Distance	0.3756