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Report generated at 2020-05-21 12:02:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	176654432	192499798
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114795372	188890798
Mapped(QC-failed)	0	0
% Mapped	64.9800	98.1300
Paired	176654432	192499798
Paired(QC-failed)	0	0
Read1	88327216	96249899
Read1(QC-failed)	0	0
Read2	88327216	96249899
Read2(QC-failed)	0	0
Properly Paired	112386184	186811687
Properly Paired(QC-failed)	0	0
% Properly Paired	63.6200	97.0500
With itself	113245729	188072528
With itself(QC-failed)	0	0
Singletons	1549643	818270
Singletons(QC-failed)	0	0
% Singleton	0.8800	0.4300
Diff. Chroms	282788	400341
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	49763271	81972176
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	424068	587245
Paired Opt. Dupes	2118	4247
% Dupes/100	0.0085	0.0072

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49760686	81931652
Distinct Read Pairs	49336652	81345140
One Read Pair	48916633	80765524
Two Read Pairs	416115	573498
NRF = Distinct/Total	0.9915	0.9928
PBC1 = OnePair/Distinct	0.9915	0.9929
PBC2 = OnePair/TwoPair	117.5556	140.8297

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	98678406	162769862
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98678406	162769862
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	98678406	162769862
Paired(QC-failed)	0	0
Read1	49339203	81384931
Read1(QC-failed)	0	0
Read2	49339203	81384931
Read2(QC-failed)	0	0
Properly Paired	98678406	162769862
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	98678406	162769862
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	240475
Np	0
N optimal	240475
N conservative	240475
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.	0.1901
Phantom Peak	50
Corr. Phantom Peak	0.2274
Argmin. Corr.	1500
Min. Corr.	0.1734
NSC	1.0960
RSC	0.3086

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	0.3197

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	0.1957
AUC	0.4959
CHANCE divergence	0.1557
Elbow Point	0.0000
JS Distance	0.6820
Synthetic AUC	0.4995
Synthetic Elbow Point	0.2214
Synthetic JS Distance	0.4079