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Report generated at 2019-10-12 23:47:35

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	99539622	95805330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94961797	91174239
Mapped(QC-failed)	0	0
% Mapped	95.4000	95.1700
Paired	99539622	95805330
Paired(QC-failed)	0	0
Read1	49769811	47902665
Read1(QC-failed)	0	0
Read2	49769811	47902665
Read2(QC-failed)	0	0
Properly Paired	91109908	87029614
Properly Paired(QC-failed)	0	0
% Properly Paired	91.5300	90.8400
With itself	91706635	88132031
With itself(QC-failed)	0	0
Singletons	3255162	3042208
Singletons(QC-failed)	0	0
% Singleton	3.2700	3.1800
Diff. Chroms	302179	677774
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	38718595	36289675
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11768563	346498
Paired Opt. Dupes	4434	3852
% Dupes/100	0.3040	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	38717843	36261516
Distinct Read Pairs	26949484	35915541
One Read Pair	18601695	35581631
Two Read Pairs	5906689	326616
NRF = Distinct/Total	0.6960	0.9905
PBC1 = OnePair/Distinct	0.6902	0.9907
PBC2 = OnePair/TwoPair	3.1493	108.9403

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	53900064	71886354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53900064	71886354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	53900064	71886354
Paired(QC-failed)	0	0
Read1	26950032	35943177
Read1(QC-failed)	0	0
Read2	26950032	35943177
Read2(QC-failed)	0	0
Properly Paired	53900064	71886354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	53900064	71886354
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	59590
Np	0
N optimal	59590
N conservative	59590
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.	135
Corr. Est. Fragment Len.	0.1510
Phantom Peak	50
Corr. Phantom Peak	0.1554
Argmin. Corr.	1500
Min. Corr.	0.1471
NSC	1.0266
RSC	0.4728

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	0.0420

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	0.2844
AUC	0.4944
CHANCE divergence	0.1181
Elbow Point	0.0000
JS Distance	0.5644
Synthetic AUC	0.4974
Synthetic Elbow Point	0.0734
Synthetic JS Distance	0.2604