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Report generated at 2020-05-20 23:22:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	87057672	176817872
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	53912240	173073807
Mapped(QC-failed)	0	0
% Mapped	61.9300	97.8800
Paired	87057672	176817872
Paired(QC-failed)	0	0
Read1	43528836	88408936
Read1(QC-failed)	0	0
Read2	43528836	88408936
Read2(QC-failed)	0	0
Properly Paired	52605180	171003617
Properly Paired(QC-failed)	0	0
% Properly Paired	60.4300	96.7100
With itself	52988467	172265942
With itself(QC-failed)	0	0
Singletons	923773	807865
Singletons(QC-failed)	0	0
% Singleton	1.0600	0.4600
Diff. Chroms	137133	503576
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	23205546	75220911
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	167965	718589
Paired Opt. Dupes	1322	2612
% Dupes/100	0.0072	0.0096

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	23200160	75167057
Distinct Read Pairs	23032256	74449701
One Read Pair	22865452	73740092
Two Read Pairs	165732	702144
NRF = Distinct/Total	0.9928	0.9905
PBC1 = OnePair/Distinct	0.9928	0.9905
PBC2 = OnePair/TwoPair	137.9664	105.0213

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	46075162	149004644
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	46075162	149004644
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	46075162	149004644
Paired(QC-failed)	0	0
Read1	23037581	74502322
Read1(QC-failed)	0	0
Read2	23037581	74502322
Read2(QC-failed)	0	0
Properly Paired	46075162	149004644
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	46075162	149004644
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	41454
Np	0
N optimal	41454
N conservative	41454
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.	125
Corr. Est. Fragment Len.	0.1985
Phantom Peak	50
Corr. Phantom Peak	0.2391
Argmin. Corr.	1500
Min. Corr.	0.1638
NSC	1.2113
RSC	0.4603

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	0.1630

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	0.1977
AUC	0.4940
CHANCE divergence	0.2141
Elbow Point	0.0000
JS Distance	0.6466
Synthetic AUC	0.5078
Synthetic Elbow Point	0.1742
Synthetic JS Distance	0.3809