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Report generated at 2019-10-12 23:34:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	82046766	88801120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79763333	86768459
Mapped(QC-failed)	0	0
% Mapped	97.2200	97.7100
Paired	82046766	88801120
Paired(QC-failed)	0	0
Read1	41023383	44400560
Read1(QC-failed)	0	0
Read2	41023383	44400560
Read2(QC-failed)	0	0
Properly Paired	79433003	85806359
Properly Paired(QC-failed)	0	0
% Properly Paired	96.8100	96.6300
With itself	79554855	86430737
With itself(QC-failed)	0	0
Singletons	208478	337722
Singletons(QC-failed)	0	0
% Singleton	0.2500	0.3800
Diff. Chroms	42915	102712
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	37100468	37886939
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3351683	723026
Paired Opt. Dupes	2615	3740
% Dupes/100	0.0903	0.0191

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37098908	37657060
Distinct Read Pairs	33747369	36953214
One Read Pair	30681536	36265585
Two Read Pairs	2804356	673617
NRF = Distinct/Total	0.9097	0.9813
PBC1 = OnePair/Distinct	0.9092	0.9814
PBC2 = OnePair/TwoPair	10.9407	53.8371

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	67497570	74327826
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67497570	74327826
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	67497570	74327826
Paired(QC-failed)	0	0
Read1	33748785	37163913
Read1(QC-failed)	0	0
Read2	33748785	37163913
Read2(QC-failed)	0	0
Properly Paired	67497570	74327826
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	67497570	74327826
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	173419
Np	0
N optimal	173419
N conservative	173419
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.	185
Corr. Est. Fragment Len.	0.1986
Phantom Peak	55
Corr. Phantom Peak	0.1905
Argmin. Corr.	1500
Min. Corr.	0.1788
NSC	1.1111
RSC	1.6922

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	0.3912

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	0.1722
AUC	0.4950
CHANCE divergence	0.1783
Elbow Point	0.0000
JS Distance	0.7147
Synthetic AUC	0.5036
Synthetic Elbow Point	0.2925
Synthetic JS Distance	0.4402