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Report generated at 2019-10-30 13:00:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	69995176	143714130
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67128140	141651275
Mapped(QC-failed)	0	0
% Mapped	95.9000	98.5600
Paired	69995176	143714130
Paired(QC-failed)	0	0
Read1	34997588	71857065
Read1(QC-failed)	0	0
Read2	34997588	71857065
Read2(QC-failed)	0	0
Properly Paired	65786288	136021403
Properly Paired(QC-failed)	0	0
% Properly Paired	93.9900	94.6500
With itself	66468073	140589137
With itself(QC-failed)	0	0
Singletons	660067	1062138
Singletons(QC-failed)	0	0
% Singleton	0.9400	0.7400
Diff. Chroms	476283	3177801
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	29520221	56070460
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5503055	6270525
Paired Opt. Dupes	23839	24403
% Dupes/100	0.1864	0.1118

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29517809	55969749
Distinct Read Pairs	24015156	49713031
One Read Pair	19384031	44051001
Two Read Pairs	3882276	5120262
NRF = Distinct/Total	0.8136	0.8882
PBC1 = OnePair/Distinct	0.8072	0.8861
PBC2 = OnePair/TwoPair	4.9930	8.6033

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	48034332	99599870
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48034332	99599870
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	48034332	99599870
Paired(QC-failed)	0	0
Read1	24017166	49799935
Read1(QC-failed)	0	0
Read2	24017166	49799935
Read2(QC-failed)	0	0
Properly Paired	48034332	99599870
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	48034332	99599870
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	107753
Np	0
N optimal	107753
N conservative	107753
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.	195
Corr. Est. Fragment Len.	0.2066
Phantom Peak	55
Corr. Phantom Peak	0.1996
Argmin. Corr.	1500
Min. Corr.	0.1737
NSC	1.1893
RSC	1.2680

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	0.4365

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	0.1388
AUC	0.4928
CHANCE divergence	0.2654
Elbow Point	0.0000
JS Distance	0.7555
Synthetic AUC	0.5026
Synthetic Elbow Point	0.3475
Synthetic JS Distance	0.4747