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Report generated at 2020-07-09 22:58:48

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	115355766	139755050
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114346783	137561007
Mapped(QC-failed)	0	0
% Mapped	99.1300	98.4300
Paired	115355766	139755050
Paired(QC-failed)	0	0
Read1	57677883	69877525
Read1(QC-failed)	0	0
Read2	57677883	69877525
Read2(QC-failed)	0	0
Properly Paired	113222706	132606533
Properly Paired(QC-failed)	0	0
% Properly Paired	98.1500	94.8800
With itself	113886771	136829005
With itself(QC-failed)	0	0
Singletons	460012	732002
Singletons(QC-failed)	0	0
% Singleton	0.4000	0.5200
Diff. Chroms	111087	310461
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	52552651	58306381
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	685010	449204
Paired Opt. Dupes	2934	3926
% Dupes/100	0.0130	0.0077

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	52544412	58283535
Distinct Read Pairs	51859736	57836429
One Read Pair	51193105	57413097
Two Read Pairs	650743	414907
NRF = Distinct/Total	0.9870	0.9923
PBC1 = OnePair/Distinct	0.9871	0.9927
PBC2 = OnePair/TwoPair	78.6687	138.3758

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	103735282	115714354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103735282	115714354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	103735282	115714354
Paired(QC-failed)	0	0
Read1	51867641	57857177
Read1(QC-failed)	0	0
Read2	51867641	57857177
Read2(QC-failed)	0	0
Properly Paired	103735282	115714354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	103735282	115714354
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	213903
Np	0
N optimal	213903
N conservative	213903
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.	150
Corr. Est. Fragment Len.	0.1824
Phantom Peak	45
Corr. Phantom Peak	0.1790
Argmin. Corr.	1500
Min. Corr.	0.1716
NSC	1.0632
RSC	1.4672

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	0.4431

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	0.2050
AUC	0.4960
CHANCE divergence	0.1108
Elbow Point	0.0000
JS Distance	0.7514
Synthetic AUC	0.5072
Synthetic Elbow Point	0.2885
Synthetic JS Distance	0.4063