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Report generated at 2020-05-13 11:19:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	57924786	65266666
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49399574	62068581
Mapped(QC-failed)	0	0
% Mapped	85.2800	95.1000
Paired	57924786	65266666
Paired(QC-failed)	0	0
Read1	28962393	32633333
Read1(QC-failed)	0	0
Read2	28962393	32633333
Read2(QC-failed)	0	0
Properly Paired	48013076	52881751
Properly Paired(QC-failed)	0	0
% Properly Paired	82.8900	81.0200
With itself	48634458	60433888
With itself(QC-failed)	0	0
Singletons	765116	1634693
Singletons(QC-failed)	0	0
% Singleton	1.3200	2.5000
Diff. Chroms	421092	5291648
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	21382824	20779273
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	176083	269236
Paired Opt. Dupes	3274	2954
% Dupes/100	0.0082	0.0130

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	21382470	20779235
Distinct Read Pairs	21206390	20509999
One Read Pair	21031566	20243741
Two Read Pairs	173578	263299
NRF = Distinct/Total	0.9918	0.9870
PBC1 = OnePair/Distinct	0.9918	0.9870
PBC2 = OnePair/TwoPair	121.1649	76.8850

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	42413482	41020074
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	42413482	41020074
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	42413482	41020074
Paired(QC-failed)	0	0
Read1	21206741	20510037
Read1(QC-failed)	0	0
Read2	21206741	20510037
Read2(QC-failed)	0	0
Properly Paired	42413482	41020074
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	42413482	41020074
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	136633
Np	0
N optimal	136633
N conservative	136633
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.	260
Corr. Est. Fragment Len.	0.2199
Phantom Peak	50
Corr. Phantom Peak	0.2147
Argmin. Corr.	1500
Min. Corr.	0.1968
NSC	1.1171
RSC	1.2886

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	0.3584

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	0.1061
AUC	0.4937
CHANCE divergence	0.4666
Elbow Point	0.0000
JS Distance	0.7393
Synthetic AUC	0.4999
Synthetic Elbow Point	0.1349
Synthetic JS Distance	0.4535