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Report generated at 2019-10-31 12:51:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	89950472	258600350
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85260320	255308360
Mapped(QC-failed)	0	0
% Mapped	94.7900	98.7300
Paired	89950472	258600350
Paired(QC-failed)	0	0
Read1	44975236	129300175
Read1(QC-failed)	0	0
Read2	44975236	129300175
Read2(QC-failed)	0	0
Properly Paired	84296292	246805576
Properly Paired(QC-failed)	0	0
% Properly Paired	93.7100	95.4400
With itself	84894968	253638863
With itself(QC-failed)	0	0
Singletons	365352	1669497
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.6500
Diff. Chroms	83107	3939809
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	35661784	102636351
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	23651044	13145537
Paired Opt. Dupes	8609	27145
% Dupes/100	0.6632	0.1281

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35658100	102579949
Distinct Read Pairs	12009519	89443009
One Read Pair	4052098	77822807
Two Read Pairs	2593834	10274703
NRF = Distinct/Total	0.3368	0.8719
PBC1 = OnePair/Distinct	0.3374	0.8701
PBC2 = OnePair/TwoPair	1.5622	7.5742

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	24021480	178981628
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	24021480	178981628
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	24021480	178981628
Paired(QC-failed)	0	0
Read1	12010740	89490814
Read1(QC-failed)	0	0
Read2	12010740	89490814
Read2(QC-failed)	0	0
Properly Paired	24021480	178981628
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	24021480	178981628
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	59997
Np	0
N optimal	59997
N conservative	59997
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.	0.1023
Phantom Peak	50
Corr. Phantom Peak	0.1061
Argmin. Corr.	1500
Min. Corr.	0.0910
NSC	1.1242
RSC	0.7463

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	0.1828

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	0.2133
AUC	0.4899
CHANCE divergence	0.2255
Elbow Point	0.0000
JS Distance	0.6112
Synthetic AUC	0.5012
Synthetic Elbow Point	0.2495
Synthetic JS Distance	0.3364