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Report generated at 2020-07-10 01:19:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	81049080	139755050
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	80015122	137561007
Mapped(QC-failed)	0	0
% Mapped	98.7200	98.4300
Paired	81049080	139755050
Paired(QC-failed)	0	0
Read1	40524540	69877525
Read1(QC-failed)	0	0
Read2	40524540	69877525
Read2(QC-failed)	0	0
Properly Paired	78534760	132606533
Properly Paired(QC-failed)	0	0
% Properly Paired	96.9000	94.8800
With itself	79596593	136829005
With itself(QC-failed)	0	0
Singletons	418529	732002
Singletons(QC-failed)	0	0
% Singleton	0.5200	0.5200
Diff. Chroms	37653	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	35732892	58306381
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1965839	449204
Paired Opt. Dupes	3542	3926
% Dupes/100	0.0550	0.0077

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35722753	58283535
Distinct Read Pairs	33757677	57836429
One Read Pair	31926218	57413097
Two Read Pairs	1727437	414907
NRF = Distinct/Total	0.9450	0.9923
PBC1 = OnePair/Distinct	0.9457	0.9927
PBC2 = OnePair/TwoPair	18.4818	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	67534106	115714354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67534106	115714354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	67534106	115714354
Paired(QC-failed)	0	0
Read1	33767053	57857177
Read1(QC-failed)	0	0
Read2	33767053	57857177
Read2(QC-failed)	0	0
Properly Paired	67534106	115714354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	67534106	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	101414
Np	0
N optimal	101414
N conservative	101414
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.	0.1909
Phantom Peak	50
Corr. Phantom Peak	0.1785
Argmin. Corr.	1500
Min. Corr.	0.1642
NSC	1.1625
RSC	1.8709

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	0.2672

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	0.2419
AUC	0.4951
CHANCE divergence	0.1124
Elbow Point	0.0000
JS Distance	0.6865
Synthetic AUC	0.4990
Synthetic Elbow Point	0.2439
Synthetic JS Distance	0.3522