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Report generated at 2020-05-14 23:00:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	186259140	75348014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	171426643	72639776
Mapped(QC-failed)	0	0
% Mapped	92.0400	96.4100
Paired	186259140	75348014
Paired(QC-failed)	0	0
Read1	93129570	37674007
Read1(QC-failed)	0	0
Read2	93129570	37674007
Read2(QC-failed)	0	0
Properly Paired	168288933	70114889
Properly Paired(QC-failed)	0	0
% Properly Paired	90.3500	93.0500
With itself	170122266	71857749
With itself(QC-failed)	0	0
Singletons	1304377	782027
Singletons(QC-failed)	0	0
% Singleton	0.7000	1.0400
Diff. Chroms	787278	1077494
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	71851924	30082479
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	684668	117823
Paired Opt. Dupes	3192	447
% Dupes/100	0.0095	0.0039

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	71845857	30056490
Distinct Read Pairs	71161268	29938925
One Read Pair	70485511	29821774
Two Read Pairs	667254	116742
NRF = Distinct/Total	0.9905	0.9961
PBC1 = OnePair/Distinct	0.9905	0.9961
PBC2 = OnePair/TwoPair	105.6352	255.4503

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	142334512	59929312
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	142334512	59929312
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	142334512	59929312
Paired(QC-failed)	0	0
Read1	71167256	29964656
Read1(QC-failed)	0	0
Read2	71167256	29964656
Read2(QC-failed)	0	0
Properly Paired	142334512	59929312
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	142334512	59929312
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	53095
Np	0
N optimal	53095
N conservative	53095
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.	125
Corr. Est. Fragment Len.	0.1871
Phantom Peak	50
Corr. Phantom Peak	0.2085
Argmin. Corr.	1500
Min. Corr.	0.1784
NSC	1.0486
RSC	0.2880

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	0.0383

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	0.2801
AUC	0.4966
CHANCE divergence	0.0932
Elbow Point	0.0000
JS Distance	0.6012
Synthetic AUC	0.4985
Synthetic Elbow Point	0.0600
Synthetic JS Distance	0.2859