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Report generated at 2020-07-10 02:54:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	107573566	166164986
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106409280	163647560
Mapped(QC-failed)	0	0
% Mapped	98.9200	98.4800
Paired	107573566	166164986
Paired(QC-failed)	0	0
Read1	53786783	83082493
Read1(QC-failed)	0	0
Read2	53786783	83082493
Read2(QC-failed)	0	0
Properly Paired	105377666	159369723
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9600	95.9100
With itself	106091756	162885733
With itself(QC-failed)	0	0
Singletons	317524	761827
Singletons(QC-failed)	0	0
% Singleton	0.3000	0.4600
Diff. Chroms	47233	172110
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	48750934	70155381
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	625905	564841
Paired Opt. Dupes	3094	3752
% Dupes/100	0.0128	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48745078	70119762
Distinct Read Pairs	48119406	69558647
One Read Pair	47507810	69027662
Two Read Pairs	600345	519769
NRF = Distinct/Total	0.9872	0.9920
PBC1 = OnePair/Distinct	0.9873	0.9924
PBC2 = OnePair/TwoPair	79.1342	132.8045

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	96250058	139181080
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96250058	139181080
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	96250058	139181080
Paired(QC-failed)	0	0
Read1	48125029	69590540
Read1(QC-failed)	0	0
Read2	48125029	69590540
Read2(QC-failed)	0	0
Properly Paired	96250058	139181080
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	96250058	139181080
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	215317
Np	0
N optimal	215317
N conservative	215317
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.	0.1767
Phantom Peak	45
Corr. Phantom Peak	0.1758
Argmin. Corr.	1500
Min. Corr.	0.1687
NSC	1.0473
RSC	1.1324

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	0.2917

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	0.2507
AUC	0.4959
CHANCE divergence	0.1054
Elbow Point	0.0000
JS Distance	0.6840
Synthetic AUC	0.4984
Synthetic Elbow Point	0.2070
Synthetic JS Distance	0.3270