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Report generated at 2019-10-12 22:40:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	89029866	95303484
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87080120	93698887
Mapped(QC-failed)	0	0
% Mapped	97.8100	98.3200
Paired	89029866	95303484
Paired(QC-failed)	0	0
Read1	44514933	47651742
Read1(QC-failed)	0	0
Read2	44514933	47651742
Read2(QC-failed)	0	0
Properly Paired	86101032	92817374
Properly Paired(QC-failed)	0	0
% Properly Paired	96.7100	97.3900
With itself	86600579	93255357
With itself(QC-failed)	0	0
Singletons	479541	443530
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.4700
Diff. Chroms	178299	88278
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	39009985	40669559
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3185450	762016
Paired Opt. Dupes	5578	5994
% Dupes/100	0.0817	0.0187

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39009599	40650316
Distinct Read Pairs	35824176	39888802
One Read Pair	32887949	39146114
Two Read Pairs	2705324	727016
NRF = Distinct/Total	0.9183	0.9813
PBC1 = OnePair/Distinct	0.9180	0.9814
PBC2 = OnePair/TwoPair	12.1568	53.8449

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	71649070	79815086
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71649070	79815086
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	71649070	79815086
Paired(QC-failed)	0	0
Read1	35824535	39907543
Read1(QC-failed)	0	0
Read2	35824535	39907543
Read2(QC-failed)	0	0
Properly Paired	71649070	79815086
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	71649070	79815086
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	137186
Np	0
N optimal	137186
N conservative	137186
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.	200
Corr. Est. Fragment Len.	0.1904
Phantom Peak	50
Corr. Phantom Peak	0.1925
Argmin. Corr.	1500
Min. Corr.	0.1784
NSC	1.0675
RSC	0.8559

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	0.4979

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	0.1623
AUC	0.4952
CHANCE divergence	0.1436
Elbow Point	0.0000
JS Distance	0.7876
Synthetic AUC	0.5053
Synthetic Elbow Point	0.3097
Synthetic JS Distance	0.4744