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Report generated at 2020-07-10 04:12:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	113732340	166164986
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112181517	163647560
Mapped(QC-failed)	0	0
% Mapped	98.6400	98.4800
Paired	113732340	166164986
Paired(QC-failed)	0	0
Read1	56866170	83082493
Read1(QC-failed)	0	0
Read2	56866170	83082493
Read2(QC-failed)	0	0
Properly Paired	110619106	159369723
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2600	95.9100
With itself	111714654	162885733
With itself(QC-failed)	0	0
Singletons	466863	761827
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.4600
Diff. Chroms	73524	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	48391097	70155381
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	598882	564841
Paired Opt. Dupes	2542	3752
% Dupes/100	0.0124	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48367226	70119762
Distinct Read Pairs	47769903	69558647
One Read Pair	47190017	69027662
Two Read Pairs	568957	519769
NRF = Distinct/Total	0.9877	0.9920
PBC1 = OnePair/Distinct	0.9879	0.9924
PBC2 = OnePair/TwoPair	82.9413	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	95584430	139181080
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95584430	139181080
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	95584430	139181080
Paired(QC-failed)	0	0
Read1	47792215	69590540
Read1(QC-failed)	0	0
Read2	47792215	69590540
Read2(QC-failed)	0	0
Properly Paired	95584430	139181080
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	95584430	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	122213
Np	0
N optimal	122213
N conservative	122213
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.	0.1782
Phantom Peak	50
Corr. Phantom Peak	0.1831
Argmin. Corr.	1500
Min. Corr.	0.1721
NSC	1.0350
RSC	0.5479

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	0.0748

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	0.2882
AUC	0.4958
CHANCE divergence	0.1014
Elbow Point	0.0000
JS Distance	0.5791
Synthetic AUC	0.4999
Synthetic Elbow Point	0.1252
Synthetic JS Distance	0.2648