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Report generated at 2020-05-14 23:16:44

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	117587962	113987742
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110158012	105961159
Mapped(QC-failed)	0	0
% Mapped	93.6800	92.9600
Paired	117587962	113987742
Paired(QC-failed)	0	0
Read1	58793981	56993871
Read1(QC-failed)	0	0
Read2	58793981	56993871
Read2(QC-failed)	0	0
Properly Paired	105842485	90037210
Properly Paired(QC-failed)	0	0
% Properly Paired	90.0100	78.9900
With itself	108474617	102013829
With itself(QC-failed)	0	0
Singletons	1683395	3947330
Singletons(QC-failed)	0	0
% Singleton	1.4300	3.4600
Diff. Chroms	2097856	8799460
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	46749600	33432972
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	537462	558302
Paired Opt. Dupes	1160	789
% Dupes/100	0.0115	0.0167

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46749340	33432710
Distinct Read Pairs	46211881	32874411
One Read Pair	45681135	32324786
Two Read Pairs	524131	541092
NRF = Distinct/Total	0.9885	0.9833
PBC1 = OnePair/Distinct	0.9885	0.9833
PBC2 = OnePair/TwoPair	87.1560	59.7399

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	92424276	65749340
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92424276	65749340
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	92424276	65749340
Paired(QC-failed)	0	0
Read1	46212138	32874670
Read1(QC-failed)	0	0
Read2	46212138	32874670
Read2(QC-failed)	0	0
Properly Paired	92424276	65749340
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	92424276	65749340
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	203701
Np	0
N optimal	203701
N conservative	203701
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.	0.2510
Phantom Peak	55
Corr. Phantom Peak	0.2318
Argmin. Corr.	1500
Min. Corr.	0.2037
NSC	1.2322
RSC	1.6845

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	0.4491

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	0.0763
AUC	0.4958
CHANCE divergence	0.4976
Elbow Point	0.0000
JS Distance	0.7954
Synthetic AUC	0.4988
Synthetic Elbow Point	0.1216
Synthetic JS Distance	0.5416