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Report generated at 2019-10-13 03:38:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115211096	84831728
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112103487	78378634
Mapped(QC-failed)	0	0
% Mapped	97.3000	92.3900
Paired	115211096	84831728
Paired(QC-failed)	0	0
Read1	57605548	42415864
Read1(QC-failed)	0	0
Read2	57605548	42415864
Read2(QC-failed)	0	0
Properly Paired	110828737	77370313
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2000	91.2000
With itself	111029736	78051674
With itself(QC-failed)	0	0
Singletons	1073751	326960
Singletons(QC-failed)	0	0
% Singleton	0.9300	0.3900
Diff. Chroms	64831	132697
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	50826420	34106970
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5414197	361659
Paired Opt. Dupes	2990	2500
% Dupes/100	0.1065	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50820446	33930415
Distinct Read Pairs	45406931	33579942
One Read Pair	40492377	33235626
Two Read Pairs	4457361	339365
NRF = Distinct/Total	0.8935	0.9897
PBC1 = OnePair/Distinct	0.8918	0.9897
PBC2 = OnePair/TwoPair	9.0844	97.9347

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	90824446	67490622
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90824446	67490622
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	90824446	67490622
Paired(QC-failed)	0	0
Read1	45412223	33745311
Read1(QC-failed)	0	0
Read2	45412223	33745311
Read2(QC-failed)	0	0
Properly Paired	90824446	67490622
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	90824446	67490622
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	221397
Np	0
N optimal	221397
N conservative	221397
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.	185
Corr. Est. Fragment Len.	0.1970
Phantom Peak	50
Corr. Phantom Peak	0.1960
Argmin. Corr.	1500
Min. Corr.	0.1799
NSC	1.0951
RSC	1.0568

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	0.4996

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	0.1588
AUC	0.4957
CHANCE divergence	0.1423
Elbow Point	0.0000
JS Distance	0.7716
Synthetic AUC	0.4979
Synthetic Elbow Point	0.3444
Synthetic JS Distance	0.4808