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Report generated at 2019-10-13 22:03:28

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	136032742	137158696
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	132213703	133265587
Mapped(QC-failed)	0	0
% Mapped	97.1900	97.1600
Paired	136032742	137158696
Paired(QC-failed)	0	0
Read1	68016371	68579348
Read1(QC-failed)	0	0
Read2	68016371	68579348
Read2(QC-failed)	0	0
Properly Paired	129690087	131002100
Properly Paired(QC-failed)	0	0
% Properly Paired	95.3400	95.5100
With itself	130283746	131535060
With itself(QC-failed)	0	0
Singletons	1929957	1730527
Singletons(QC-failed)	0	0
% Singleton	1.4200	1.2600
Diff. Chroms	159391	98144
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	54851655	54747675
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1924265	1493596
Paired Opt. Dupes	7805	7775
% Dupes/100	0.0351	0.0273

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	54849884	54683489
Distinct Read Pairs	52925686	53193120
One Read Pair	51070285	51758910
Two Read Pairs	1791682	1391528
NRF = Distinct/Total	0.9649	0.9727
PBC1 = OnePair/Distinct	0.9649	0.9730
PBC2 = OnePair/TwoPair	28.5041	37.1957

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	105854780	106508158
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105854780	106508158
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	105854780	106508158
Paired(QC-failed)	0	0
Read1	52927390	53254079
Read1(QC-failed)	0	0
Read2	52927390	53254079
Read2(QC-failed)	0	0
Properly Paired	105854780	106508158
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	105854780	106508158
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	131613
Np	0
N optimal	131613
N conservative	131613
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.	105
Corr. Est. Fragment Len.	0.1815
Phantom Peak	50
Corr. Phantom Peak	0.1940
Argmin. Corr.	1500
Min. Corr.	0.1759
NSC	1.0317
RSC	0.3091

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	0.2106

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	0.2641
AUC	0.4960
CHANCE divergence	0.1030
Elbow Point	0.0000
JS Distance	0.6535
Synthetic AUC	0.4973
Synthetic Elbow Point	0.1345
Synthetic JS Distance	0.3104