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Report generated at 2020-12-04 07:40:29

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	149754508	148269018
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	146932925	143500908
Mapped(QC-failed)	0	0
% Mapped	98.1200	96.7800
Paired	149754508	148269018
Paired(QC-failed)	0	0
Read1	74877254	74134509
Read1(QC-failed)	0	0
Read2	74877254	74134509
Read2(QC-failed)	0	0
Properly Paired	144621847	140225987
Properly Paired(QC-failed)	0	0
% Properly Paired	96.5700	94.5800
With itself	145850065	141622671
With itself(QC-failed)	0	0
Singletons	1082860	1878237
Singletons(QC-failed)	0	0
% Singleton	0.7200	1.2700
Diff. Chroms	689594	652729
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	64802038	59090669
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	625034	523701
Paired Opt. Dupes	9048	14446
% Dupes/100	0.0096	0.0089

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	64745707	57674075
Distinct Read Pairs	64121828	57472830
One Read Pair	63503672	57272993
Two Read Pairs	612557	198503
NRF = Distinct/Total	0.9904	0.9965
PBC1 = OnePair/Distinct	0.9904	0.9965
PBC2 = OnePair/TwoPair	103.6698	288.5246

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	128354008	117133936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	128354008	117133936
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	128354008	117133936
Paired(QC-failed)	0	0
Read1	64177004	58566968
Read1(QC-failed)	0	0
Read2	64177004	58566968
Read2(QC-failed)	0	0
Properly Paired	128354008	117133936
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	128354008	117133936
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	88847
Np	0
N optimal	88847
N conservative	88847
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.	140
Corr. Est. Fragment Len.	0.2059
Phantom Peak	50
Corr. Phantom Peak	0.2116
Argmin. Corr.	1500
Min. Corr.	0.1880
NSC	1.0952
RSC	0.7580

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	0.2883

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	0.2445
AUC	0.4964
CHANCE divergence	0.0961
Elbow Point	0.0000
JS Distance	0.7240
Synthetic AUC	0.5019
Synthetic Elbow Point	0.2771
Synthetic JS Distance	0.3697