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Report generated at 2020-05-28 14:49:16

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	100058214	129938162
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	99548532	127236885
Mapped(QC-failed)	0	0
% Mapped	99.4900	97.9200
Paired	100058214	129938162
Paired(QC-failed)	0	0
Read1	50029107	64969081
Read1(QC-failed)	0	0
Read2	50029107	64969081
Read2(QC-failed)	0	0
Properly Paired	99031234	124171445
Properly Paired(QC-failed)	0	0
% Properly Paired	98.9700	95.5600
With itself	99260102	126465025
With itself(QC-failed)	0	0
Singletons	288430	771860
Singletons(QC-failed)	0	0
% Singleton	0.2900	0.5900
Diff. Chroms	32545	239141
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	46819920	54765466
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1148905	445838
Paired Opt. Dupes	1436	1418
% Dupes/100	0.0245	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	46793664	54644116
Distinct Read Pairs	45647954	54251549
One Read Pair	44633896	53877110
Two Read Pairs	920879	366240
NRF = Distinct/Total	0.9755	0.9928
PBC1 = OnePair/Distinct	0.9778	0.9931
PBC2 = OnePair/TwoPair	48.4688	147.1088

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	91342030	108639256
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91342030	108639256
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	91342030	108639256
Paired(QC-failed)	0	0
Read1	45671015	54319628
Read1(QC-failed)	0	0
Read2	45671015	54319628
Read2(QC-failed)	0	0
Properly Paired	91342030	108639256
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	91342030	108639256
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	112917
Np	0
N optimal	112917
N conservative	112917
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.	0.2465
Phantom Peak	55
Corr. Phantom Peak	0.2174
Argmin. Corr.	1500
Min. Corr.	0.1871
NSC	1.3174
RSC	1.9633

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	0.5723

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	0.1238
AUC	0.4957
CHANCE divergence	0.1618
Elbow Point	0.0000
JS Distance	0.8353
Synthetic AUC	0.5039
Synthetic Elbow Point	0.4332
Synthetic JS Distance	0.5575