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Report generated at 2020-12-03 22:27:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98153698	148269018
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97095045	143500908
Mapped(QC-failed)	0	0
% Mapped	98.9200	96.7800
Paired	98153698	148269018
Paired(QC-failed)	0	0
Read1	49076849	74134509
Read1(QC-failed)	0	0
Read2	49076849	74134509
Read2(QC-failed)	0	0
Properly Paired	96177919	140225987
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9900	94.5800
With itself	96765760	141622671
With itself(QC-failed)	0	0
Singletons	329285	1878237
Singletons(QC-failed)	0	0
% Singleton	0.3400	1.2700
Diff. Chroms	319816	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	42843585	59090669
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3882258	523701
Paired Opt. Dupes	4720	14446
% Dupes/100	0.0906	0.0089

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42822721	57674075
Distinct Read Pairs	38942445	57472830
One Read Pair	35377583	57272993
Two Read Pairs	3272132	198503
NRF = Distinct/Total	0.9094	0.9965
PBC1 = OnePair/Distinct	0.9085	0.9965
PBC2 = OnePair/TwoPair	10.8118	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	77922654	117133936
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	77922654	117133936
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	77922654	117133936
Paired(QC-failed)	0	0
Read1	38961327	58566968
Read1(QC-failed)	0	0
Read2	38961327	58566968
Read2(QC-failed)	0	0
Properly Paired	77922654	117133936
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	77922654	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	52107
Np	0
N optimal	52107
N conservative	52107
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.	255
Corr. Est. Fragment Len.	0.1769
Phantom Peak	50
Corr. Phantom Peak	0.1836
Argmin. Corr.	1500
Min. Corr.	0.1705
NSC	1.0376
RSC	0.4903

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	0.1527

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	0.2886
AUC	0.4954
CHANCE divergence	0.1006
Elbow Point	0.0000
JS Distance	0.5955
Synthetic AUC	0.4989
Synthetic Elbow Point	0.1779
Synthetic JS Distance	0.2779