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Report generated at 2019-11-03 07:32:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	62918006	196869810
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61775704	192216298
Mapped(QC-failed)	0	0
% Mapped	98.1800	97.6400
Paired	62918006	196869810
Paired(QC-failed)	0	0
Read1	31459003	98434905
Read1(QC-failed)	0	0
Read2	31459003	98434905
Read2(QC-failed)	0	0
Properly Paired	61016934	187412851
Properly Paired(QC-failed)	0	0
% Properly Paired	96.9800	95.2000
With itself	61435262	190908042
With itself(QC-failed)	0	0
Singletons	340442	1308256
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.6600
Diff. Chroms	168792	1377453
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	27735313	83348574
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1960814	1654003
Paired Opt. Dupes	5041	15356
% Dupes/100	0.0707	0.0198

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27719506	83232910
Distinct Read Pairs	25759904	81583711
One Read Pair	23919039	79958418
Two Read Pairs	1728475	1602927
NRF = Distinct/Total	0.9293	0.9802
PBC1 = OnePair/Distinct	0.9285	0.9801
PBC2 = OnePair/TwoPair	13.8382	49.8828

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	51548998	163389142
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	51548998	163389142
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	51548998	163389142
Paired(QC-failed)	0	0
Read1	25774499	81694571
Read1(QC-failed)	0	0
Read2	25774499	81694571
Read2(QC-failed)	0	0
Properly Paired	51548998	163389142
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	51548998	163389142
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	28336
Np	0
N optimal	28336
N conservative	28336
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.	205
Corr. Est. Fragment Len.	0.3457
Phantom Peak	55
Corr. Phantom Peak	0.3192
Argmin. Corr.	1500
Min. Corr.	0.1761
NSC	1.9635
RSC	1.1849

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	0.4499

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	0.1699
AUC	0.4943
CHANCE divergence	0.1361
Elbow Point	0.0000
JS Distance	0.8425
Synthetic AUC	0.4953
Synthetic Elbow Point	0.4601
Synthetic JS Distance	0.5119