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Report generated at 2019-10-12 21:16:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	129847806	84831728
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78079505	78378634
Mapped(QC-failed)	0	0
% Mapped	60.1300	92.3900
Paired	129847806	84831728
Paired(QC-failed)	0	0
Read1	64923903	42415864
Read1(QC-failed)	0	0
Read2	64923903	42415864
Read2(QC-failed)	0	0
Properly Paired	76788724	77370313
Properly Paired(QC-failed)	0	0
% Properly Paired	59.1400	91.2000
With itself	77595720	78051674
With itself(QC-failed)	0	0
Singletons	483785	326960
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.3900
Diff. Chroms	43983	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	35649239	34106970
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	12312188	361659
Paired Opt. Dupes	4987	2500
% Dupes/100	0.3454	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35634568	33930415
Distinct Read Pairs	23327770	33579942
One Read Pair	14787854	33235626
Two Read Pairs	5828666	339365
NRF = Distinct/Total	0.6546	0.9897
PBC1 = OnePair/Distinct	0.6339	0.9897
PBC2 = OnePair/TwoPair	2.5371	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	46674102	67490622
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46674102	67490622
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	46674102	67490622
Paired(QC-failed)	0	0
Read1	23337051	33745311
Read1(QC-failed)	0	0
Read2	23337051	33745311
Read2(QC-failed)	0	0
Properly Paired	46674102	67490622
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	46674102	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	52847
Np	0
N optimal	52847
N conservative	52847
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.	130
Corr. Est. Fragment Len.	0.4380
Phantom Peak	55
Corr. Phantom Peak	0.3791
Argmin. Corr.	1500
Min. Corr.	0.1578
NSC	2.7755
RSC	1.2664

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	0.6167

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	0.0950
AUC	0.4940
CHANCE divergence	0.2595
Elbow Point	0.0000
JS Distance	0.9024
Synthetic AUC	0.5022
Synthetic Elbow Point	0.5534
Synthetic JS Distance	0.6231