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Report generated at 2019-10-25 19:29:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	114220794	175533488
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	111042027	173335768
Mapped(QC-failed)	0	0
% Mapped	97.2200	98.7500
Paired	114220794	175533488
Paired(QC-failed)	0	0
Read1	57110397	87766744
Read1(QC-failed)	0	0
Read2	57110397	87766744
Read2(QC-failed)	0	0
Properly Paired	109259197	163307962
Properly Paired(QC-failed)	0	0
% Properly Paired	95.6600	93.0400
With itself	110422829	171954161
With itself(QC-failed)	0	0
Singletons	619198	1381607
Singletons(QC-failed)	0	0
% Singleton	0.5400	0.7900
Diff. Chroms	759648	6449643
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	48976482	68252842
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10505735	5232871
Paired Opt. Dupes	7346	11154
% Dupes/100	0.2145	0.0767

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48975488	68242424
Distinct Read Pairs	38469969	63010354
One Read Pair	29914213	58070357
Two Read Pairs	6932239	4666317
NRF = Distinct/Total	0.7855	0.9233
PBC1 = OnePair/Distinct	0.7776	0.9216
PBC2 = OnePair/TwoPair	4.3152	12.4446

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	76941494	126039942
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76941494	126039942
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76941494	126039942
Paired(QC-failed)	0	0
Read1	38470747	63019971
Read1(QC-failed)	0	0
Read2	38470747	63019971
Read2(QC-failed)	0	0
Properly Paired	76941494	126039942
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76941494	126039942
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	64483
Np	0
N optimal	64483
N conservative	64483
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.	0.3889
Phantom Peak	55
Corr. Phantom Peak	0.3493
Argmin. Corr.	1500
Min. Corr.	0.1990
NSC	1.9544
RSC	1.2639

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	0.6321

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	0.0914
AUC	0.4943
CHANCE divergence	0.2098
Elbow Point	0.0000
JS Distance	0.8810
Synthetic AUC	0.5051
Synthetic Elbow Point	0.5658
Synthetic JS Distance	0.6281