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Report generated at 2020-06-06 01:28:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	121976446	117975254
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	118394350	115587149
Mapped(QC-failed)	0	0
% Mapped	97.0600	97.9800
Paired	121976446	117975254
Paired(QC-failed)	0	0
Read1	60988223	58987627
Read1(QC-failed)	0	0
Read2	60988223	58987627
Read2(QC-failed)	0	0
Properly Paired	116907387	114336090
Properly Paired(QC-failed)	0	0
% Properly Paired	95.8400	96.9200
With itself	117579895	114956123
With itself(QC-failed)	0	0
Singletons	814455	631026
Singletons(QC-failed)	0	0
% Singleton	0.6700	0.5300
Diff. Chroms	131414	214233
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	48942499	50038328
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3920258	1990115
Paired Opt. Dupes	12278	11498
% Dupes/100	0.0801	0.0398

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48940505	49998318
Distinct Read Pairs	45020415	48010251
One Read Pair	41388050	46077673
Two Read Pairs	3376994	1886322
NRF = Distinct/Total	0.9199	0.9602
PBC1 = OnePair/Distinct	0.9193	0.9597
PBC2 = OnePair/TwoPair	12.2559	24.4273

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	90044482	96096426
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90044482	96096426
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	90044482	96096426
Paired(QC-failed)	0	0
Read1	45022241	48048213
Read1(QC-failed)	0	0
Read2	45022241	48048213
Read2(QC-failed)	0	0
Properly Paired	90044482	96096426
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	90044482	96096426
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	71732
Np	0
N optimal	71732
N conservative	71732
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.	120
Corr. Est. Fragment Len.	0.1860
Phantom Peak	50
Corr. Phantom Peak	0.2129
Argmin. Corr.	1500
Min. Corr.	0.1783
NSC	1.0432
RSC	0.2224

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	0.0759

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	0.2891
AUC	0.4957
CHANCE divergence	0.1051
Elbow Point	0.0000
JS Distance	0.5585
Synthetic AUC	0.5043
Synthetic Elbow Point	0.0849
Synthetic JS Distance	0.2688