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Report generated at 2020-05-20 14:38:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	96995254	136200922
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94607854	132760866
Mapped(QC-failed)	0	0
% Mapped	97.5400	97.4700
Paired	96995254	136200922
Paired(QC-failed)	0	0
Read1	48497627	68100461
Read1(QC-failed)	0	0
Read2	48497627	68100461
Read2(QC-failed)	0	0
Properly Paired	93544885	130688000
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4400	95.9500
With itself	94291828	132096613
With itself(QC-failed)	0	0
Singletons	316026	664253
Singletons(QC-failed)	0	0
% Singleton	0.3300	0.4900
Diff. Chroms	463513	663242
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	42902363	56907844
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	246750	250818
Paired Opt. Dupes	1438	2178
% Dupes/100	0.0058	0.0044

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42898079	56865752
Distinct Read Pairs	42651352	56615485
One Read Pair	42406016	56366456
Two Read Pairs	243947	247819
NRF = Distinct/Total	0.9942	0.9956
PBC1 = OnePair/Distinct	0.9942	0.9956
PBC2 = OnePair/TwoPair	173.8329	227.4501

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	85311226	113314052
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85311226	113314052
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	85311226	113314052
Paired(QC-failed)	0	0
Read1	42655613	56657026
Read1(QC-failed)	0	0
Read2	42655613	56657026
Read2(QC-failed)	0	0
Properly Paired	85311226	113314052
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	85311226	113314052
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	149653
Np	0
N optimal	149653
N conservative	149653
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.	180
Corr. Est. Fragment Len.	0.1936
Phantom Peak	50
Corr. Phantom Peak	0.1951
Argmin. Corr.	1500
Min. Corr.	0.1830
NSC	1.0583
RSC	0.8776

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	0.3200

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	0.1967
AUC	0.4956
CHANCE divergence	0.1325
Elbow Point	0.0000
JS Distance	0.7014
Synthetic AUC	0.5018
Synthetic Elbow Point	0.2421
Synthetic JS Distance	0.4131