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Report generated at 2020-04-08 14:46:49

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	67248950	91343384
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	37861691	89445671
Mapped(QC-failed)	0	0
% Mapped	56.3000	97.9200
Paired	67248950	91343384
Paired(QC-failed)	0	0
Read1	33624475	45671692
Read1(QC-failed)	0	0
Read2	33624475	45671692
Read2(QC-failed)	0	0
Properly Paired	33088856	87213841
Properly Paired(QC-failed)	0	0
% Properly Paired	49.2000	95.4800
With itself	36849606	88898599
With itself(QC-failed)	0	0
Singletons	1012085	547072
Singletons(QC-failed)	0	0
% Singleton	1.5000	0.6000
Diff. Chroms	120404	153716
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	14893819	38419123
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8474367	536213
Paired Opt. Dupes	3883	12817
% Dupes/100	0.5690	0.0140

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	14893614	38404764
Distinct Read Pairs	6419345	37868795
One Read Pair	3511994	37344268
Two Read Pairs	1242025	515141
NRF = Distinct/Total	0.4310	0.9860
PBC1 = OnePair/Distinct	0.5471	0.9861
PBC2 = OnePair/TwoPair	2.8276	72.4933

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	12838904	75765820
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	12838904	75765820
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	12838904	75765820
Paired(QC-failed)	0	0
Read1	6419452	37882910
Read1(QC-failed)	0	0
Read2	6419452	37882910
Read2(QC-failed)	0	0
Properly Paired	12838904	75765820
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	12838904	75765820
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	92327
Np	0
N optimal	92327
N conservative	92327
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.	75
Corr. Est. Fragment Len.	0.0800
Phantom Peak	50
Corr. Phantom Peak	0.0672
Argmin. Corr.	1500
Min. Corr.	0.0589
NSC	1.3583
RSC	2.5569

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	0.1445

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	0.1575
AUC	0.4886
CHANCE divergence	0.4556
Elbow Point	0.0000
JS Distance	0.7162
Synthetic AUC	0.4966
Synthetic Elbow Point	0.1650
Synthetic JS Distance	0.3025