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Report generated at 2020-07-10 08:58:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	131525876	166164986
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	124596292	163647560
Mapped(QC-failed)	0	0
% Mapped	94.7300	98.4800
Paired	131525876	166164986
Paired(QC-failed)	0	0
Read1	65762938	83082493
Read1(QC-failed)	0	0
Read2	65762938	83082493
Read2(QC-failed)	0	0
Properly Paired	122160296	159369723
Properly Paired(QC-failed)	0	0
% Properly Paired	92.8800	95.9100
With itself	123688658	162885733
With itself(QC-failed)	0	0
Singletons	907634	761827
Singletons(QC-failed)	0	0
% Singleton	0.6900	0.4600
Diff. Chroms	126765	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	48198298	70155381
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2735764	564841
Paired Opt. Dupes	2571	3752
% Dupes/100	0.0568	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48186687	70119762
Distinct Read Pairs	45451929	69558647
One Read Pair	42935868	69027662
Two Read Pairs	2384329	519769
NRF = Distinct/Total	0.9432	0.9920
PBC1 = OnePair/Distinct	0.9446	0.9924
PBC2 = OnePair/TwoPair	18.0075	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	90925068	139181080
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90925068	139181080
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	90925068	139181080
Paired(QC-failed)	0	0
Read1	45462534	69590540
Read1(QC-failed)	0	0
Read2	45462534	69590540
Read2(QC-failed)	0	0
Properly Paired	90925068	139181080
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	90925068	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	160529
Np	0
N optimal	160529
N conservative	160529
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.	115
Corr. Est. Fragment Len.	0.1814
Phantom Peak	50
Corr. Phantom Peak	0.1997
Argmin. Corr.	1500
Min. Corr.	0.1726
NSC	1.0511
RSC	0.3254

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	0.1536

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	0.2806
AUC	0.4957
CHANCE divergence	0.0992
Elbow Point	0.0000
JS Distance	0.6196
Synthetic AUC	0.5030
Synthetic Elbow Point	0.1505
Synthetic JS Distance	0.2795