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Report generated at 2020-07-10 06:43:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	168240748	139755050
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	165427791	137561007
Mapped(QC-failed)	0	0
% Mapped	98.3300	98.4300
Paired	168240748	139755050
Paired(QC-failed)	0	0
Read1	84120374	69877525
Read1(QC-failed)	0	0
Read2	84120374	69877525
Read2(QC-failed)	0	0
Properly Paired	159063438	132606533
Properly Paired(QC-failed)	0	0
% Properly Paired	94.5500	94.8800
With itself	164420127	136829005
With itself(QC-failed)	0	0
Singletons	1007664	732002
Singletons(QC-failed)	0	0
% Singleton	0.6000	0.5200
Diff. Chroms	217964	310461
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	68758712	58306381
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1442703	449204
Paired Opt. Dupes	3684	3926
% Dupes/100	0.0210	0.0077

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	68737063	58283535
Distinct Read Pairs	67296393	57836429
One Read Pair	65915111	57413097
Two Read Pairs	1335840	414907
NRF = Distinct/Total	0.9790	0.9923
PBC1 = OnePair/Distinct	0.9795	0.9927
PBC2 = OnePair/TwoPair	49.3436	138.3758

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	134632018	115714354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	134632018	115714354
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	134632018	115714354
Paired(QC-failed)	0	0
Read1	67316009	57857177
Read1(QC-failed)	0	0
Read2	67316009	57857177
Read2(QC-failed)	0	0
Properly Paired	134632018	115714354
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	134632018	115714354
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	224526
Np	0
N optimal	224526
N conservative	224526
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.	0.1846
Phantom Peak	50
Corr. Phantom Peak	0.1882
Argmin. Corr.	1500
Min. Corr.	0.1775
NSC	1.0401
RSC	0.6632

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	0.1758

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	0.2489
AUC	0.4965
CHANCE divergence	0.1027
Elbow Point	0.0000
JS Distance	0.6134
Synthetic AUC	0.5052
Synthetic Elbow Point	0.1908
Synthetic JS Distance	0.3343