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Report generated at 2020-05-15 09:42:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	160619298	144095950
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	156532207	133456854
Mapped(QC-failed)	0	0
% Mapped	97.4600	92.6200
Paired	160619298	144095950
Paired(QC-failed)	0	0
Read1	80309649	72047975
Read1(QC-failed)	0	0
Read2	80309649	72047975
Read2(QC-failed)	0	0
Properly Paired	152294180	100085786
Properly Paired(QC-failed)	0	0
% Properly Paired	94.8200	69.4600
With itself	155284886	127614780
With itself(QC-failed)	0	0
Singletons	1247321	5842074
Singletons(QC-failed)	0	0
% Singleton	0.7800	4.0500
Diff. Chroms	2163833	21841128
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	68867709	33283608
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	513725	401960
Paired Opt. Dupes	2051	902
% Dupes/100	0.0075	0.0121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	68853652	33264694
Distinct Read Pairs	68340062	32863263
One Read Pair	67830431	32466574
Two Read Pairs	505710	392011
NRF = Distinct/Total	0.9925	0.9879
PBC1 = OnePair/Distinct	0.9925	0.9879
PBC2 = OnePair/TwoPair	134.1291	82.8206

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	136707968	65763296
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	136707968	65763296
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	136707968	65763296
Paired(QC-failed)	0	0
Read1	68353984	32881648
Read1(QC-failed)	0	0
Read2	68353984	32881648
Read2(QC-failed)	0	0
Properly Paired	136707968	65763296
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	136707968	65763296
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	204181
Np	0
N optimal	204181
N conservative	204181
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.	0.2119
Phantom Peak	50
Corr. Phantom Peak	0.2095
Argmin. Corr.	1500
Min. Corr.	0.1890
NSC	1.1213
RSC	1.1149

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	0.4105

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	0.1360
AUC	0.4965
CHANCE divergence	0.2102
Elbow Point	0.0000
JS Distance	0.7586
Synthetic AUC	0.5036
Synthetic Elbow Point	0.1848
Synthetic JS Distance	0.5064