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Report generated at 2020-05-18 16:17:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	76337608	188531594
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	73681986	183497192
Mapped(QC-failed)	0	0
% Mapped	96.5200	97.3300
Paired	76337608	188531594
Paired(QC-failed)	0	0
Read1	38168804	94265797
Read1(QC-failed)	0	0
Read2	38168804	94265797
Read2(QC-failed)	0	0
Properly Paired	72844653	180692140
Properly Paired(QC-failed)	0	0
% Properly Paired	95.4200	95.8400
With itself	73388767	182539954
With itself(QC-failed)	0	0
Singletons	293219	957238
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.5100
Diff. Chroms	313999	942066
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	33051776	78941456
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	158257	448927
Paired Opt. Dupes	1266	2929
% Dupes/100	0.0048	0.0057

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33048309	78883545
Distinct Read Pairs	32890066	78435677
One Read Pair	32732494	77991934
Two Read Pairs	156903	439949
NRF = Distinct/Total	0.9952	0.9943
PBC1 = OnePair/Distinct	0.9952	0.9943
PBC2 = OnePair/TwoPair	208.6161	177.2749

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	65787038	156985058
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65787038	156985058
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	65787038	156985058
Paired(QC-failed)	0	0
Read1	32893519	78492529
Read1(QC-failed)	0	0
Read2	32893519	78492529
Read2(QC-failed)	0	0
Properly Paired	65787038	156985058
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	65787038	156985058
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	100350
Np	0
N optimal	100350
N conservative	100350
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.	145
Corr. Est. Fragment Len.	0.1861
Phantom Peak	50
Corr. Phantom Peak	0.1913
Argmin. Corr.	1500
Min. Corr.	0.1772
NSC	1.0502
RSC	0.6283

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	0.1997

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	0.2357
AUC	0.4950
CHANCE divergence	0.1208
Elbow Point	0.0000
JS Distance	0.6564
Synthetic AUC	0.4970
Synthetic Elbow Point	0.1877
Synthetic JS Distance	0.3492