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Report generated at 2020-06-05 09:37:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	41291840	77888856
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	35707759	76061398
Mapped(QC-failed)	0	0
% Mapped	86.4800	97.6500
Paired	41291840	77888856
Paired(QC-failed)	0	0
Read1	20645920	38944428
Read1(QC-failed)	0	0
Read2	20645920	38944428
Read2(QC-failed)	0	0
Properly Paired	34388214	75336051
Properly Paired(QC-failed)	0	0
% Properly Paired	83.2800	96.7200
With itself	34863945	75672411
With itself(QC-failed)	0	0
Singletons	843814	388987
Singletons(QC-failed)	0	0
% Singleton	2.0400	0.5000
Diff. Chroms	103983	70563
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	13380796	32868058
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6936119	449274
Paired Opt. Dupes	4017	9598
% Dupes/100	0.5184	0.0137

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	13380080	32844128
Distinct Read Pairs	6444265	32395430
One Read Pair	3582159	31957931
Two Read Pairs	1315663	429179
NRF = Distinct/Total	0.4816	0.9863
PBC1 = OnePair/Distinct	0.5559	0.9865
PBC2 = OnePair/TwoPair	2.7227	74.4629

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	12889354	64837568
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	12889354	64837568
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	12889354	64837568
Paired(QC-failed)	0	0
Read1	6444677	32418784
Read1(QC-failed)	0	0
Read2	6444677	32418784
Read2(QC-failed)	0	0
Properly Paired	12889354	64837568
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	12889354	64837568
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	67525
Np	0
N optimal	67525
N conservative	67525
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.	140
Corr. Est. Fragment Len.	0.1423
Phantom Peak	50
Corr. Phantom Peak	0.1727
Argmin. Corr.	1500
Min. Corr.	0.1113
NSC	1.2776
RSC	0.5041

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	0.1729

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	0.1558
AUC	0.4887
CHANCE divergence	0.4296
Elbow Point	0.0000
JS Distance	0.7057
Synthetic AUC	0.4976
Synthetic Elbow Point	0.1883
Synthetic JS Distance	0.3352