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Report generated at 2020-05-02 10:29:53

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	47318880	56737366
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	44914680	53249558
Mapped(QC-failed)	0	0
% Mapped	94.9200	93.8500
Paired	47318880	56737366
Paired(QC-failed)	0	0
Read1	23659440	28368683
Read1(QC-failed)	0	0
Read2	23659440	28368683
Read2(QC-failed)	0	0
Properly Paired	43269643	46970465
Properly Paired(QC-failed)	0	0
% Properly Paired	91.4400	82.7900
With itself	44319905	52253794
With itself(QC-failed)	0	0
Singletons	594775	995764
Singletons(QC-failed)	0	0
% Singleton	1.2600	1.7600
Diff. Chroms	709661	3675402
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	18855249	19151739
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	125200	222856
Paired Opt. Dupes	1949	2619
% Dupes/100	0.0066	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	18855111	19151685
Distinct Read Pairs	18729914	18928829
One Read Pair	18605346	18708139
Two Read Pairs	123944	218547
NRF = Distinct/Total	0.9934	0.9884
PBC1 = OnePair/Distinct	0.9933	0.9883
PBC2 = OnePair/TwoPair	150.1109	85.6024

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	37460098	37857766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	37460098	37857766
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	37460098	37857766
Paired(QC-failed)	0	0
Read1	18730049	18928883
Read1(QC-failed)	0	0
Read2	18730049	18928883
Read2(QC-failed)	0	0
Properly Paired	37460098	37857766
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	37460098	37857766
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	89430
Np	0
N optimal	89430
N conservative	89430
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.	270
Corr. Est. Fragment Len.	0.2045
Phantom Peak	50
Corr. Phantom Peak	0.1940
Argmin. Corr.	1500
Min. Corr.	0.1825
NSC	1.1206
RSC	1.9180

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	0.1268

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	0.1197
AUC	0.4933
CHANCE divergence	0.4927
Elbow Point	0.0000
JS Distance	0.7117
Synthetic AUC	0.5070
Synthetic Elbow Point	0.0428
Synthetic JS Distance	0.3946