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Report generated at 2021-02-06 05:37:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	117943950	126012150
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116689433	124283922
Mapped(QC-failed)	0	0
% Mapped	98.9400	98.6300
Paired	117943950	126012150
Paired(QC-failed)	0	0
Read1	58971975	63006075
Read1(QC-failed)	0	0
Read2	58971975	63006075
Read2(QC-failed)	0	0
Properly Paired	115656123	120756755
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0600	95.8300
With itself	116126763	123573365
With itself(QC-failed)	0	0
Singletons	562670	710557
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5600
Diff. Chroms	66404	156752
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	50073148	52700713
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	513473	316838
Paired Opt. Dupes	76808	77810
% Dupes/100	0.0103	0.0060

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	50057709	52686084
Distinct Read Pairs	49544818	52369782
One Read Pair	49038649	52065772
Two Read Pairs	500282	298643
NRF = Distinct/Total	0.9898	0.9940
PBC1 = OnePair/Distinct	0.9898	0.9942
PBC2 = OnePair/TwoPair	98.0220	174.3412

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	99119350	104767750
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99119350	104767750
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	99119350	104767750
Paired(QC-failed)	0	0
Read1	49559675	52383875
Read1(QC-failed)	0	0
Read2	49559675	52383875
Read2(QC-failed)	0	0
Properly Paired	99119350	104767750
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	99119350	104767750
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	97094
Np	0
N optimal	97094
N conservative	97094
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.	115
Corr. Est. Fragment Len.	0.1733
Phantom Peak	50
Corr. Phantom Peak	0.1783
Argmin. Corr.	1500
Min. Corr.	0.1686
NSC	1.0277
RSC	0.4818

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	0.0590

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	0.3162
AUC	0.4958
CHANCE divergence	0.1001
Elbow Point	0.0000
JS Distance	0.5485
Synthetic AUC	0.5005
Synthetic Elbow Point	0.0562
Synthetic JS Distance	0.2200