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Report generated at 2020-07-09 13:55:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	78296714	107365242
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	77418082	105642663
Mapped(QC-failed)	0	0
% Mapped	98.8800	98.4000
Paired	78296714	107365242
Paired(QC-failed)	0	0
Read1	39148357	53682621
Read1(QC-failed)	0	0
Read2	39148357	53682621
Read2(QC-failed)	0	0
Properly Paired	76782369	101883703
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0700	94.8900
With itself	77053246	105057441
With itself(QC-failed)	0	0
Singletons	364836	585222
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.5500
Diff. Chroms	23159	159211
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	35469485	44782756
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3641643	288172
Paired Opt. Dupes	3572	2765
% Dupes/100	0.1027	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35458071	44758305
Distinct Read Pairs	31817785	44472498
One Read Pair	28671703	44200745
Two Read Pairs	2806410	266773
NRF = Distinct/Total	0.8973	0.9936
PBC1 = OnePair/Distinct	0.9011	0.9939
PBC2 = OnePair/TwoPair	10.2165	165.6867

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	63655684	88989168
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	63655684	88989168
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	63655684	88989168
Paired(QC-failed)	0	0
Read1	31827842	44494584
Read1(QC-failed)	0	0
Read2	31827842	44494584
Read2(QC-failed)	0	0
Properly Paired	63655684	88989168
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	63655684	88989168
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	101306
Np	0
N optimal	101306
N conservative	101306
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.	150
Corr. Est. Fragment Len.	0.2496
Phantom Peak	55
Corr. Phantom Peak	0.1947
Argmin. Corr.	1500
Min. Corr.	0.1605
NSC	1.5547
RSC	2.6027

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	0.4804

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	0.1574
AUC	0.4949
CHANCE divergence	0.1416
Elbow Point	0.0000
JS Distance	0.8256
Synthetic AUC	0.4977
Synthetic Elbow Point	0.4094
Synthetic JS Distance	0.5038