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Report generated at 2020-05-21 00:29:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	143855786	185333438
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108173757	179322251
Mapped(QC-failed)	0	0
% Mapped	75.2000	96.7600
Paired	143855786	185333438
Paired(QC-failed)	0	0
Read1	71927893	92666719
Read1(QC-failed)	0	0
Read2	71927893	92666719
Read2(QC-failed)	0	0
Properly Paired	106661089	177236646
Properly Paired(QC-failed)	0	0
% Properly Paired	74.1400	95.6300
With itself	107145236	178226497
With itself(QC-failed)	0	0
Singletons	1028521	1095754
Singletons(QC-failed)	0	0
% Singleton	0.7100	0.5900
Diff. Chroms	188279	321793
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	48343557	76478349
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	406733	700148
Paired Opt. Dupes	2275	1938
% Dupes/100	0.0084	0.0092

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48341813	76473537
Distinct Read Pairs	47935094	75773440
One Read Pair	47531832	75080087
Two Read Pairs	399850	686711
NRF = Distinct/Total	0.9916	0.9908
PBC1 = OnePair/Distinct	0.9916	0.9909
PBC2 = OnePair/TwoPair	118.8742	109.3329

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	95873648	151556402
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95873648	151556402
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	95873648	151556402
Paired(QC-failed)	0	0
Read1	47936824	75778201
Read1(QC-failed)	0	0
Read2	47936824	75778201
Read2(QC-failed)	0	0
Properly Paired	95873648	151556402
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	95873648	151556402
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	165753
Np	0
N optimal	165753
N conservative	165753
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.	160
Corr. Est. Fragment Len.	0.1968
Phantom Peak	50
Corr. Phantom Peak	0.2134
Argmin. Corr.	1500
Min. Corr.	0.1807
NSC	1.0891
RSC	0.4931

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	0.4187

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	0.1846
AUC	0.4959
CHANCE divergence	0.1203
Elbow Point	0.0000
JS Distance	0.7588
Synthetic AUC	0.5032
Synthetic Elbow Point	0.2692
Synthetic JS Distance	0.4440