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Report generated at 2020-05-27 14:03:03

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	181678758	199291734
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	131295156	192758941
Mapped(QC-failed)	0	0
% Mapped	72.2700	96.7200
Paired	181678758	199291734
Paired(QC-failed)	0	0
Read1	90839379	99645867
Read1(QC-failed)	0	0
Read2	90839379	99645867
Read2(QC-failed)	0	0
Properly Paired	129331870	190351557
Properly Paired(QC-failed)	0	0
% Properly Paired	71.1900	95.5100
With itself	130064043	191591556
With itself(QC-failed)	0	0
Singletons	1231113	1167385
Singletons(QC-failed)	0	0
% Singleton	0.6800	0.5900
Diff. Chroms	241363	372346
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	56293740	82947353
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	647148	947217
Paired Opt. Dupes	1829	3959
% Dupes/100	0.0115	0.0114

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	56288098	82921397
Distinct Read Pairs	55641029	81974628
One Read Pair	55002062	81039698
Two Read Pairs	630977	923351
NRF = Distinct/Total	0.9885	0.9886
PBC1 = OnePair/Distinct	0.9885	0.9886
PBC2 = OnePair/TwoPair	87.1697	87.7669

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	111293184	164000272
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	111293184	164000272
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	111293184	164000272
Paired(QC-failed)	0	0
Read1	55646592	82000136
Read1(QC-failed)	0	0
Read2	55646592	82000136
Read2(QC-failed)	0	0
Properly Paired	111293184	164000272
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	111293184	164000272
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	105810
Np	0
N optimal	105810
N conservative	105810
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.	0.1790
Phantom Peak	50
Corr. Phantom Peak	0.2043
Argmin. Corr.	1500
Min. Corr.	0.1707
NSC	1.0484
RSC	0.2460

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	0.0666

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	0.2672
AUC	0.4961
CHANCE divergence	0.1009
Elbow Point	0.0000
JS Distance	0.6048
Synthetic AUC	0.5007
Synthetic Elbow Point	0.0637
Synthetic JS Distance	0.3022