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Report generated at 2021-10-10 07:18:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	147365804	135940090
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	145860758	134333469
Mapped(QC-failed)	0	0
% Mapped	98.9800	98.8200
Paired	147365804	135940090
Paired(QC-failed)	0	0
Read1	73682902	67970045
Read1(QC-failed)	0	0
Read2	73682902	67970045
Read2(QC-failed)	0	0
Properly Paired	144441945	131959627
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0200	97.0700
With itself	145104657	133529071
With itself(QC-failed)	0	0
Singletons	756101	804398
Singletons(QC-failed)	0	0
% Singleton	0.5100	0.5900
Diff. Chroms	350487	898860
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	62884951	55193949
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6215638	3483873
Paired Opt. Dupes	59627	49939
% Dupes/100	0.0988	0.0631

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	62884254	55175675
Distinct Read Pairs	56668679	51692963
One Read Pair	50914870	48296105
Two Read Pairs	5325041	3315273
NRF = Distinct/Total	0.9012	0.9369
PBC1 = OnePair/Distinct	0.8985	0.9343
PBC2 = OnePair/TwoPair	9.5614	14.5678

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	113338626	103420152
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	113338626	103420152
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	113338626	103420152
Paired(QC-failed)	0	0
Read1	56669313	51710076
Read1(QC-failed)	0	0
Read2	56669313	51710076
Read2(QC-failed)	0	0
Properly Paired	113338626	103420152
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	113338626	103420152
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	135221
Np	0
N optimal	135221
N conservative	135221
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.	215
Corr. Est. Fragment Len.	0.2014
Phantom Peak	50
Corr. Phantom Peak	0.2028
Argmin. Corr.	1500
Min. Corr.	0.1850
NSC	1.0887
RSC	0.9228

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	0.5897

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	0.1509
AUC	0.4953
CHANCE divergence	0.1184
Elbow Point	0.0000
JS Distance	0.8384
Synthetic AUC	0.5027
Synthetic Elbow Point	0.4143
Synthetic JS Distance	0.5123