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Report generated at 2020-06-10 10:56:24

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65527532	136472354
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	64947745	133975828
Mapped(QC-failed)	0	0
% Mapped	99.1200	98.1700
Paired	65527532	136472354
Paired(QC-failed)	0	0
Read1	32763766	68236177
Read1(QC-failed)	0	0
Read2	32763766	68236177
Read2(QC-failed)	0	0
Properly Paired	64511930	130521106
Properly Paired(QC-failed)	0	0
% Properly Paired	98.4500	95.6400
With itself	64689040	133246152
With itself(QC-failed)	0	0
Singletons	258705	729676
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.5300
Diff. Chroms	37127	190651
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	29168416	57086227
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	250802	492281
Paired Opt. Dupes	1117	1233
% Dupes/100	0.0086	0.0086

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	29150066	56946845
Distinct Read Pairs	28900077	56516291
One Read Pair	28655465	56111544
Two Read Pairs	239872	395440
NRF = Distinct/Total	0.9914	0.9924
PBC1 = OnePair/Distinct	0.9915	0.9928
PBC2 = OnePair/TwoPair	119.4615	141.8965

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	57835228	113187892
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57835228	113187892
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	57835228	113187892
Paired(QC-failed)	0	0
Read1	28917614	56593946
Read1(QC-failed)	0	0
Read2	28917614	56593946
Read2(QC-failed)	0	0
Properly Paired	57835228	113187892
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	57835228	113187892
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	117548
Np	0
N optimal	117548
N conservative	117548
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.	0.1840
Phantom Peak	50
Corr. Phantom Peak	0.1839
Argmin. Corr.	1500
Min. Corr.	0.1704
NSC	1.0797
RSC	1.0107

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	0.2556

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	0.2331
AUC	0.4947
CHANCE divergence	0.1150
Elbow Point	0.0000
JS Distance	0.6826
Synthetic AUC	0.4967
Synthetic Elbow Point	0.2261
Synthetic JS Distance	0.3583