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Report generated at 2019-10-30 21:16:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	81725766	194901230
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78350779	192136328
Mapped(QC-failed)	0	0
% Mapped	95.8700	98.5800
Paired	81725766	194901230
Paired(QC-failed)	0	0
Read1	40862883	97450615
Read1(QC-failed)	0	0
Read2	40862883	97450615
Read2(QC-failed)	0	0
Properly Paired	77356372	187452194
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6500	96.1800
With itself	78015131	191119169
With itself(QC-failed)	0	0
Singletons	335648	1017159
Singletons(QC-failed)	0	0
% Singleton	0.4100	0.5200
Diff. Chroms	393313	2127070
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	34126312	77977039
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2335869	1865117
Paired Opt. Dupes	8176	13406
% Dupes/100	0.0684	0.0239

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34125992	77969017
Distinct Read Pairs	31790149	76104111
One Read Pair	29585451	74277183
Two Read Pairs	2079858	1790747
NRF = Distinct/Total	0.9316	0.9761
PBC1 = OnePair/Distinct	0.9306	0.9760
PBC2 = OnePair/TwoPair	14.2247	41.4783

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	63580886	152223844
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63580886	152223844
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	63580886	152223844
Paired(QC-failed)	0	0
Read1	31790443	76111922
Read1(QC-failed)	0	0
Read2	31790443	76111922
Read2(QC-failed)	0	0
Properly Paired	63580886	152223844
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	63580886	152223844
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	156778
Np	0
N optimal	156778
N conservative	156778
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.	145
Corr. Est. Fragment Len.	0.2144
Phantom Peak	50
Corr. Phantom Peak	0.2140
Argmin. Corr.	1500
Min. Corr.	0.1909
NSC	1.1233
RSC	1.0210

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	0.6102

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	0.1178
AUC	0.4939
CHANCE divergence	0.2109
Elbow Point	0.0000
JS Distance	0.8377
Synthetic AUC	0.5097
Synthetic Elbow Point	0.4516
Synthetic JS Distance	0.5450