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Report generated at 2021-02-07 21:14:52

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98372944	334658014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70691076	328702336
Mapped(QC-failed)	0	0
% Mapped	71.8600	98.2200
Paired	98372944	334658014
Paired(QC-failed)	0	0
Read1	49186472	167329007
Read1(QC-failed)	0	0
Read2	49186472	167329007
Read2(QC-failed)	0	0
Properly Paired	70003605	320102484
Properly Paired(QC-failed)	0	0
% Properly Paired	71.1600	95.6500
With itself	70379097	326658529
With itself(QC-failed)	0	0
Singletons	311979	2043807
Singletons(QC-failed)	0	0
% Singleton	0.3200	0.6100
Diff. Chroms	135502	620372
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	31566289	141663705
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1414351	1830718
Paired Opt. Dupes	4282	10233
% Dupes/100	0.0448	0.0129

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	31544175	141095473
Distinct Read Pairs	30131084	139340732
One Read Pair	28780681	137631421
Two Read Pairs	1290548	1682298
NRF = Distinct/Total	0.9552	0.9876
PBC1 = OnePair/Distinct	0.9552	0.9877
PBC2 = OnePair/TwoPair	22.3011	81.8116

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	60303876	279665974
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60303876	279665974
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	60303876	279665974
Paired(QC-failed)	0	0
Read1	30151938	139832987
Read1(QC-failed)	0	0
Read2	30151938	139832987
Read2(QC-failed)	0	0
Properly Paired	60303876	279665974
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	60303876	279665974
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	113019
Np	0
N optimal	113019
N conservative	113019
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.	195
Corr. Est. Fragment Len.	0.1873
Phantom Peak	50
Corr. Phantom Peak	0.1904
Argmin. Corr.	1500
Min. Corr.	0.1763
NSC	1.0620
RSC	0.7767

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	0.2787

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	0.2268
AUC	0.4947
CHANCE divergence	0.1246
Elbow Point	0.0000
JS Distance	0.6767
Synthetic AUC	0.4976
Synthetic Elbow Point	0.2811
Synthetic JS Distance	0.3661