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Report generated at 2021-03-18 13:42:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	36015406	148600262
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30426227	144098222
Mapped(QC-failed)	0	0
% Mapped	84.4800	96.9700
Paired	36015406	148600262
Paired(QC-failed)	0	0
Read1	18007703	74300131
Read1(QC-failed)	0	0
Read2	18007703	74300131
Read2(QC-failed)	0	0
Properly Paired	29823917	124201504
Properly Paired(QC-failed)	0	0
% Properly Paired	82.8100	83.5800
With itself	30254591	142351740
With itself(QC-failed)	0	0
Singletons	171636	1746482
Singletons(QC-failed)	0	0
% Singleton	0.4800	1.1800
Diff. Chroms	104198	13088864
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	13684270	55069462
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1305451	517761
Paired Opt. Dupes	2849	1468
% Dupes/100	0.0954	0.0094

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	13678840	55053291
Distinct Read Pairs	12374039	54537877
One Read Pair	11190635	54050644
Two Read Pairs	1081760	474902
NRF = Distinct/Total	0.9046	0.9906
PBC1 = OnePair/Distinct	0.9044	0.9911
PBC2 = OnePair/TwoPair	10.3448	113.8143

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	24757638	109103402
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	24757638	109103402
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	24757638	109103402
Paired(QC-failed)	0	0
Read1	12378819	54551701
Read1(QC-failed)	0	0
Read2	12378819	54551701
Read2(QC-failed)	0	0
Properly Paired	24757638	109103402
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	24757638	109103402
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	78002
Np	0
N optimal	78002
N conservative	78002
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.	0.2420
Phantom Peak	55
Corr. Phantom Peak	0.1900
Argmin. Corr.	1500
Min. Corr.	0.1510
NSC	1.6025
RSC	2.3299

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	0.4753

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	0.1214
AUC	0.4918
CHANCE divergence	0.3254
Elbow Point	0.0000
JS Distance	0.7766
Synthetic AUC	0.5109
Synthetic Elbow Point	0.4166
Synthetic JS Distance	0.5057