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Report generated at 2021-10-10 05:19:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	135924388	140797568
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	130338007	138331903
Mapped(QC-failed)	0	0
% Mapped	95.8900	98.2500
Paired	135924388	140797568
Paired(QC-failed)	0	0
Read1	67962194	70398784
Read1(QC-failed)	0	0
Read2	67962194	70398784
Read2(QC-failed)	0	0
Properly Paired	124748041	130482644
Properly Paired(QC-failed)	0	0
% Properly Paired	91.7800	92.6700
With itself	127564519	136981110
With itself(QC-failed)	0	0
Singletons	2773488	1350793
Singletons(QC-failed)	0	0
% Singleton	2.0400	0.9600
Diff. Chroms	1930654	4662721
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	53312171	54667780
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7751291	4758897
Paired Opt. Dupes	13004	8500
% Dupes/100	0.1454	0.0871

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	53298698	54581914
Distinct Read Pairs	45549318	49831729
One Read Pair	38764822	45411889
Two Read Pairs	5927998	4111745
NRF = Distinct/Total	0.8546	0.9130
PBC1 = OnePair/Distinct	0.8511	0.9113
PBC2 = OnePair/TwoPair	6.5393	11.0444

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	91121760	99817766
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91121760	99817766
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	91121760	99817766
Paired(QC-failed)	0	0
Read1	45560880	49908883
Read1(QC-failed)	0	0
Read2	45560880	49908883
Read2(QC-failed)	0	0
Properly Paired	91121760	99817766
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	91121760	99817766
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	109326
Np	0
N optimal	109326
N conservative	109326
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.	205
Corr. Est. Fragment Len.	0.1699
Phantom Peak	50
Corr. Phantom Peak	0.1756
Argmin. Corr.	1500
Min. Corr.	0.1653
NSC	1.0280
RSC	0.4484

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	0.2184

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	0.2800
AUC	0.4948
CHANCE divergence	0.1106
Elbow Point	0.0000
JS Distance	0.6344
Synthetic AUC	0.5021
Synthetic Elbow Point	0.1638
Synthetic JS Distance	0.2804