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Report generated at 2020-05-02 08:30:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	31901844	56737366
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	28357866	53249558
Mapped(QC-failed)	0	0
% Mapped	88.8900	93.8500
Paired	31901844	56737366
Paired(QC-failed)	0	0
Read1	15950922	28368683
Read1(QC-failed)	0	0
Read2	15950922	28368683
Read2(QC-failed)	0	0
Properly Paired	27630532	46970465
Properly Paired(QC-failed)	0	0
% Properly Paired	86.6100	82.7900
With itself	27931595	52253794
With itself(QC-failed)	0	0
Singletons	426271	995764
Singletons(QC-failed)	0	0
% Singleton	1.3400	1.7600
Diff. Chroms	170483	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	12329662	19151739
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	231062	222856
Paired Opt. Dupes	2709	2619
% Dupes/100	0.0187	0.0116

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	12329082	19151685
Distinct Read Pairs	12098031	18928829
One Read Pair	11870560	18708139
Two Read Pairs	223942	218547
NRF = Distinct/Total	0.9813	0.9884
PBC1 = OnePair/Distinct	0.9812	0.9883
PBC2 = OnePair/TwoPair	53.0073	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	24197200	37857766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	24197200	37857766
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	24197200	37857766
Paired(QC-failed)	0	0
Read1	12098600	18928883
Read1(QC-failed)	0	0
Read2	12098600	18928883
Read2(QC-failed)	0	0
Properly Paired	24197200	37857766
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	24197200	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	25860
Np	0
N optimal	25860
N conservative	25860
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 (14M)

	rep1
Reads	14019540
Est. Fragment Len.	250
Corr. Est. Fragment Len.	0.2930
Phantom Peak	50
Corr. Phantom Peak	0.2577
Argmin. Corr.	1500
Min. Corr.	0.1590
NSC	1.8427
RSC	1.3575

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	0.3376

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	0.1370
AUC	0.4916
CHANCE divergence	0.3509
Elbow Point	0.0000
JS Distance	0.7059
Synthetic AUC	0.5110
Synthetic Elbow Point	0.3312
Synthetic JS Distance	0.4619