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Report generated at 2020-05-22 14:07:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	72743542	127861076
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	69549222	126069958
Mapped(QC-failed)	0	0
% Mapped	95.6100	98.6000
Paired	72743542	127861076
Paired(QC-failed)	0	0
Read1	36371771	63930538
Read1(QC-failed)	0	0
Read2	36371771	63930538
Read2(QC-failed)	0	0
Properly Paired	69151061	122750247
Properly Paired(QC-failed)	0	0
% Properly Paired	95.0600	96.0000
With itself	69312249	125397302
With itself(QC-failed)	0	0
Singletons	236973	672656
Singletons(QC-failed)	0	0
% Singleton	0.3300	0.5300
Diff. Chroms	23391	127073
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	31415614	54205503
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2297364	466424
Paired Opt. Dupes	1673	4293
% Dupes/100	0.0731	0.0086

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	31404194	54190280
Distinct Read Pairs	29107552	53725300
One Read Pair	27285767	53274643
Two Read Pairs	1545723	442720
NRF = Distinct/Total	0.9269	0.9914
PBC1 = OnePair/Distinct	0.9374	0.9916
PBC2 = OnePair/TwoPair	17.6524	120.3348

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	58236500	107478158
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	58236500	107478158
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	58236500	107478158
Paired(QC-failed)	0	0
Read1	29118250	53739079
Read1(QC-failed)	0	0
Read2	29118250	53739079
Read2(QC-failed)	0	0
Properly Paired	58236500	107478158
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	58236500	107478158
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	60545
Np	0
N optimal	60545
N conservative	60545
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.	170
Corr. Est. Fragment Len.	0.2885
Phantom Peak	45
Corr. Phantom Peak	0.1984
Argmin. Corr.	1500
Min. Corr.	0.1413
NSC	2.0415
RSC	2.5773

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	0.4824

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	0.1533
AUC	0.4947
CHANCE divergence	0.1465
Elbow Point	0.0000
JS Distance	0.8446
Synthetic AUC	0.5045
Synthetic Elbow Point	0.4369
Synthetic JS Distance	0.5240