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Report generated at 2020-05-20 15:07:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	169849714	112353936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	169078898	110770243
Mapped(QC-failed)	0	0
% Mapped	99.5500	98.5900
Paired	169849714	112353936
Paired(QC-failed)	0	0
Read1	84924857	56176968
Read1(QC-failed)	0	0
Read2	84924857	56176968
Read2(QC-failed)	0	0
Properly Paired	168569706	108511153
Properly Paired(QC-failed)	0	0
% Properly Paired	99.2500	96.5800
With itself	168743522	110354562
With itself(QC-failed)	0	0
Singletons	335376	415681
Singletons(QC-failed)	0	0
% Singleton	0.2000	0.3700
Diff. Chroms	56685	150895
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	79354120	48323075
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1838196	444698
Paired Opt. Dupes	5840	3241
% Dupes/100	0.0232	0.0092

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	79348731	48311362
Distinct Read Pairs	77510718	47868098
One Read Pair	75771845	47445446
Two Read Pairs	1653602	412601
NRF = Distinct/Total	0.9768	0.9908
PBC1 = OnePair/Distinct	0.9776	0.9912
PBC2 = OnePair/TwoPair	45.8223	114.9911

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	155031848	95756754
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	155031848	95756754
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	155031848	95756754
Paired(QC-failed)	0	0
Read1	77515924	47878377
Read1(QC-failed)	0	0
Read2	77515924	47878377
Read2(QC-failed)	0	0
Properly Paired	155031848	95756754
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	155031848	95756754
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	242851
Np	0
N optimal	242851
N conservative	242851
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.	150
Corr. Est. Fragment Len.	0.1976
Phantom Peak	55
Corr. Phantom Peak	0.1874
Argmin. Corr.	1500
Min. Corr.	0.1713
NSC	1.1530
RSC	1.6285

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	0.5611

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	0.1538
AUC	0.4967
CHANCE divergence	0.1141
Elbow Point	0.0000
JS Distance	0.7878
Synthetic AUC	0.5011
Synthetic Elbow Point	0.3547
Synthetic JS Distance	0.5037