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Report generated at 2019-10-13 02:18:57

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	121510140	67430072
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117595335	65774336
Mapped(QC-failed)	0	0
% Mapped	96.7800	97.5400
Paired	121510140	67430072
Paired(QC-failed)	0	0
Read1	60755070	33715036
Read1(QC-failed)	0	0
Read2	60755070	33715036
Read2(QC-failed)	0	0
Properly Paired	115053699	65242108
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6900	96.7600
With itself	115432874	65481547
With itself(QC-failed)	0	0
Singletons	2162461	292789
Singletons(QC-failed)	0	0
% Singleton	1.7800	0.4300
Diff. Chroms	88812	63993
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	50446896	28780738
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5847299	1886510
Paired Opt. Dupes	2856	2357
% Dupes/100	0.1159	0.0655

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50445719	28752606
Distinct Read Pairs	44598558	26868268
One Read Pair	39331075	25090950
Two Read Pairs	4738878	1676042
NRF = Distinct/Total	0.8841	0.9345
PBC1 = OnePair/Distinct	0.8819	0.9339
PBC2 = OnePair/TwoPair	8.2997	14.9704

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	89199194	53788456
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89199194	53788456
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	89199194	53788456
Paired(QC-failed)	0	0
Read1	44599597	26894228
Read1(QC-failed)	0	0
Read2	44599597	26894228
Read2(QC-failed)	0	0
Properly Paired	89199194	53788456
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	89199194	53788456
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	76332
Np	0
N optimal	76332
N conservative	76332
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.	0.1730
Phantom Peak	50
Corr. Phantom Peak	0.1857
Argmin. Corr.	1500
Min. Corr.	0.1678
NSC	1.0314
RSC	0.2940

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	0.0760

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	0.3126
AUC	0.4957
CHANCE divergence	0.0997
Elbow Point	0.0000
JS Distance	0.5614
Synthetic AUC	0.5056
Synthetic Elbow Point	0.0640
Synthetic JS Distance	0.2290