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Report generated at 2020-05-20 15:32:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	140177104	118522358
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	138493771	116921431
Mapped(QC-failed)	0	0
% Mapped	98.8000	98.6500
Paired	140177104	118522358
Paired(QC-failed)	0	0
Read1	70088552	59261179
Read1(QC-failed)	0	0
Read2	70088552	59261179
Read2(QC-failed)	0	0
Properly Paired	137346452	111554301
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9800	94.1200
With itself	137794341	116290293
With itself(QC-failed)	0	0
Singletons	699430	631138
Singletons(QC-failed)	0	0
% Singleton	0.5000	0.5300
Diff. Chroms	96025	155795
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	62066330	49637685
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4270569	399141
Paired Opt. Dupes	5966	4222
% Dupes/100	0.0688	0.0080

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	62059012	49626135
Distinct Read Pairs	57789039	49227867
One Read Pair	53775448	48851116
Two Read Pairs	3780938	369226
NRF = Distinct/Total	0.9312	0.9920
PBC1 = OnePair/Distinct	0.9305	0.9923
PBC2 = OnePair/TwoPair	14.2228	132.3068

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	115591522	98477088
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115591522	98477088
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	115591522	98477088
Paired(QC-failed)	0	0
Read1	57795761	49238544
Read1(QC-failed)	0	0
Read2	57795761	49238544
Read2(QC-failed)	0	0
Properly Paired	115591522	98477088
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	115591522	98477088
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	193198
Np	0
N optimal	193198
N conservative	193198
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.	0.1782
Phantom Peak	50
Corr. Phantom Peak	0.1767
Argmin. Corr.	1500
Min. Corr.	0.1705
NSC	1.0450
RSC	1.2385

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	0.2329

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	0.2404
AUC	0.4962
CHANCE divergence	0.1019
Elbow Point	0.0000
JS Distance	0.6558
Synthetic AUC	0.5031
Synthetic Elbow Point	0.1884
Synthetic JS Distance	0.3470