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Report generated at 2020-05-20 20:43:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	94382484	192478142
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70150894	185401012
Mapped(QC-failed)	0	0
% Mapped	74.3300	96.3200
Paired	94382484	192478142
Paired(QC-failed)	0	0
Read1	47191242	96239071
Read1(QC-failed)	0	0
Read2	47191242	96239071
Read2(QC-failed)	0	0
Properly Paired	68885675	183168625
Properly Paired(QC-failed)	0	0
% Properly Paired	72.9900	95.1600
With itself	69311879	184250860
With itself(QC-failed)	0	0
Singletons	839015	1150152
Singletons(QC-failed)	0	0
% Singleton	0.8900	0.6000
Diff. Chroms	150105	298242
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	30134678	78445518
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	231880	555253
Paired Opt. Dupes	1989	2096
% Dupes/100	0.0077	0.0071

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30132864	78441301
Distinct Read Pairs	29900994	77886084
One Read Pair	29670954	77336819
Two Read Pairs	228229	543707
NRF = Distinct/Total	0.9923	0.9929
PBC1 = OnePair/Distinct	0.9923	0.9929
PBC2 = OnePair/TwoPair	130.0052	142.2399

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	59805596	155780530
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59805596	155780530
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	59805596	155780530
Paired(QC-failed)	0	0
Read1	29902798	77890265
Read1(QC-failed)	0	0
Read2	29902798	77890265
Read2(QC-failed)	0	0
Properly Paired	59805596	155780530
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	59805596	155780530
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	56512
Np	0
N optimal	56512
N conservative	56512
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.	120
Corr. Est. Fragment Len.	0.1834
Phantom Peak	50
Corr. Phantom Peak	0.2167
Argmin. Corr.	1500
Min. Corr.	0.1724
NSC	1.0644
RSC	0.2501

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	0.0804

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	0.2661
AUC	0.4947
CHANCE divergence	0.1180
Elbow Point	0.0000
JS Distance	0.5919
Synthetic AUC	0.5079
Synthetic Elbow Point	0.1115
Synthetic JS Distance	0.2964