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Report generated at 2020-07-10 13:24:42

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	110963368	110135000
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	109352657	107233350
Mapped(QC-failed)	0	0
% Mapped	98.5500	97.3700
Paired	110963368	110135000
Paired(QC-failed)	0	0
Read1	55481684	55067500
Read1(QC-failed)	0	0
Read2	55481684	55067500
Read2(QC-failed)	0	0
Properly Paired	93535614	85255224
Properly Paired(QC-failed)	0	0
% Properly Paired	84.2900	77.4100
With itself	108486068	105602140
With itself(QC-failed)	0	0
Singletons	866589	1631210
Singletons(QC-failed)	0	0
% Singleton	0.7800	1.4800
Diff. Chroms	12499809	16704113
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	42301300	37187240
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2617735	530724
Paired Opt. Dupes	2831	2167
% Dupes/100	0.0619	0.0143

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42211039	37166182
Distinct Read Pairs	39610998	36637046
One Read Pair	37217909	36123457
Two Read Pairs	2229136	503773
NRF = Distinct/Total	0.9384	0.9858
PBC1 = OnePair/Distinct	0.9396	0.9860
PBC2 = OnePair/TwoPair	16.6961	71.7058

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	79367130	73313032
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	79367130	73313032
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	79367130	73313032
Paired(QC-failed)	0	0
Read1	39683565	36656516
Read1(QC-failed)	0	0
Read2	39683565	36656516
Read2(QC-failed)	0	0
Properly Paired	79367130	73313032
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	79367130	73313032
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	86902
Np	0
N optimal	86902
N conservative	86902
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.	165
Corr. Est. Fragment Len.	0.1874
Phantom Peak	50
Corr. Phantom Peak	0.1775
Argmin. Corr.	1500
Min. Corr.	0.1630
NSC	1.1500
RSC	1.6907

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	0.2442

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	0.2532
AUC	0.4954
CHANCE divergence	0.1057
Elbow Point	0.0000
JS Distance	0.6874
Synthetic AUC	0.5010
Synthetic Elbow Point	0.2166
Synthetic JS Distance	0.3448