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Report generated at 2020-07-10 14:23:01

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	117777110	112753966
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116170010	109868487
Mapped(QC-failed)	0	0
% Mapped	98.6400	97.4400
Paired	117777110	112753966
Paired(QC-failed)	0	0
Read1	58888555	56376983
Read1(QC-failed)	0	0
Read2	58888555	56376983
Read2(QC-failed)	0	0
Properly Paired	98887926	87661066
Properly Paired(QC-failed)	0	0
% Properly Paired	83.9600	77.7500
With itself	115128883	108182157
With itself(QC-failed)	0	0
Singletons	1041127	1686330
Singletons(QC-failed)	0	0
% Singleton	0.8800	1.5000
Diff. Chroms	14048047	16951047
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	44786841	38372389
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	722398	558393
Paired Opt. Dupes	3884	2534
% Dupes/100	0.0161	0.0146

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44604376	38298911
Distinct Read Pairs	43935133	37755269
One Read Pair	43276159	37227219
Two Read Pairs	649037	517899
NRF = Distinct/Total	0.9850	0.9858
PBC1 = OnePair/Distinct	0.9850	0.9860
PBC2 = OnePair/TwoPair	66.6775	71.8812

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	88128886	75627992
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88128886	75627992
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	88128886	75627992
Paired(QC-failed)	0	0
Read1	44064443	37813996
Read1(QC-failed)	0	0
Read2	44064443	37813996
Read2(QC-failed)	0	0
Properly Paired	88128886	75627992
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	88128886	75627992
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	167657
Np	0
N optimal	167657
N conservative	167657
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.	115
Corr. Est. Fragment Len.	0.1726
Phantom Peak	50
Corr. Phantom Peak	0.1743
Argmin. Corr.	1500
Min. Corr.	0.1689
NSC	1.0223
RSC	0.6969

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	0.1160

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	0.2795
AUC	0.4957
CHANCE divergence	0.1062
Elbow Point	0.0000
JS Distance	0.6036
Synthetic AUC	0.4982
Synthetic Elbow Point	0.0930
Synthetic JS Distance	0.2781