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Report generated at 2020-06-06 02:34:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63806416	141046192
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58796279	133545822
Mapped(QC-failed)	0	0
% Mapped	92.1500	94.6800
Paired	63806416	141046192
Paired(QC-failed)	0	0
Read1	31903208	70523096
Read1(QC-failed)	0	0
Read2	31903208	70523096
Read2(QC-failed)	0	0
Properly Paired	57632522	131515734
Properly Paired(QC-failed)	0	0
% Properly Paired	90.3200	93.2400
With itself	58067398	132854680
With itself(QC-failed)	0	0
Singletons	728881	691142
Singletons(QC-failed)	0	0
% Singleton	1.1400	0.4900
Diff. Chroms	71024	243760
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	23394817	58232424
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1373959	4001234
Paired Opt. Dupes	1750	6761
% Dupes/100	0.0587	0.0687

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23388618	57912757
Distinct Read Pairs	22015025	53959656
One Read Pair	20713273	50262057
Two Read Pairs	1233412	3464802
NRF = Distinct/Total	0.9413	0.9317
PBC1 = OnePair/Distinct	0.9409	0.9315
PBC2 = OnePair/TwoPair	16.7935	14.5065

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	44041716	108462380
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44041716	108462380
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	44041716	108462380
Paired(QC-failed)	0	0
Read1	22020858	54231190
Read1(QC-failed)	0	0
Read2	22020858	54231190
Read2(QC-failed)	0	0
Properly Paired	44041716	108462380
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	44041716	108462380
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	128049
Np	0
N optimal	128049
N conservative	128049
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.	0.1809
Phantom Peak	50
Corr. Phantom Peak	0.2126
Argmin. Corr.	1500
Min. Corr.	0.1729
NSC	1.0462
RSC	0.2011

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	0.0832

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	0.2573
AUC	0.4939
CHANCE divergence	0.1539
Elbow Point	0.0000
JS Distance	0.5865
Synthetic AUC	0.5100
Synthetic Elbow Point	0.1161
Synthetic JS Distance	0.2876