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Report generated at 2020-05-21 02:46:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	118537506	177519184
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64746656	172494915
Mapped(QC-failed)	0	0
% Mapped	54.6200	97.1700
Paired	118537506	177519184
Paired(QC-failed)	0	0
Read1	59268753	88759592
Read1(QC-failed)	0	0
Read2	59268753	88759592
Read2(QC-failed)	0	0
Properly Paired	63134148	168093297
Properly Paired(QC-failed)	0	0
% Properly Paired	53.2600	94.6900
With itself	63601738	170816950
With itself(QC-failed)	0	0
Singletons	1144918	1677965
Singletons(QC-failed)	0	0
% Singleton	0.9700	0.9500
Diff. Chroms	112091	1509587
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	28070860	73622728
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	195733	559519
Paired Opt. Dupes	925	3080
% Dupes/100	0.0070	0.0076

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28062078	73528740
Distinct Read Pairs	27866427	72972791
One Read Pair	27672027	72421080
Two Read Pairs	193167	547586
NRF = Distinct/Total	0.9930	0.9924
PBC1 = OnePair/Distinct	0.9930	0.9924
PBC2 = OnePair/TwoPair	143.2544	132.2552

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	55750254	146126418
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55750254	146126418
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55750254	146126418
Paired(QC-failed)	0	0
Read1	27875127	73063209
Read1(QC-failed)	0	0
Read2	27875127	73063209
Read2(QC-failed)	0	0
Properly Paired	55750254	146126418
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55750254	146126418
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	33095
Np	0
N optimal	33095
N conservative	33095
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.	140
Corr. Est. Fragment Len.	0.2174
Phantom Peak	50
Corr. Phantom Peak	0.2555
Argmin. Corr.	1500
Min. Corr.	0.1613
NSC	1.3473
RSC	0.5951

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	0.2352

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	0.2029
AUC	0.4946
CHANCE divergence	0.1601
Elbow Point	0.0000
JS Distance	0.6777
Synthetic AUC	0.5080
Synthetic Elbow Point	0.2495
Synthetic JS Distance	0.4096