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Report generated at 2020-06-05 22:02:01

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	92778032	139413336
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	82750197	137076202
Mapped(QC-failed)	0	0
% Mapped	89.1900	98.3200
Paired	92778032	139413336
Paired(QC-failed)	0	0
Read1	46389016	69706668
Read1(QC-failed)	0	0
Read2	46389016	69706668
Read2(QC-failed)	0	0
Properly Paired	82134117	135724007
Properly Paired(QC-failed)	0	0
% Properly Paired	88.5300	97.3500
With itself	82414880	136521817
With itself(QC-failed)	0	0
Singletons	335317	554385
Singletons(QC-failed)	0	0
% Singleton	0.3600	0.4000
Diff. Chroms	63155	331576
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	37339851	59910556
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	17087357	3644145
Paired Opt. Dupes	2185	3362
% Dupes/100	0.4576	0.0608

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	37338549	59868704
Distinct Read Pairs	20251824	56228098
One Read Pair	10275545	52787644
Two Read Pairs	5613824	3261892
NRF = Distinct/Total	0.5424	0.9392
PBC1 = OnePair/Distinct	0.5074	0.9388
PBC2 = OnePair/TwoPair	1.8304	16.1831

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	40504988	112532822
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	40504988	112532822
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	40504988	112532822
Paired(QC-failed)	0	0
Read1	20252494	56266411
Read1(QC-failed)	0	0
Read2	20252494	56266411
Read2(QC-failed)	0	0
Properly Paired	40504988	112532822
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	40504988	112532822
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	136311
Np	0
N optimal	136311
N conservative	136311
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.	140
Corr. Est. Fragment Len.	0.1696
Phantom Peak	50
Corr. Phantom Peak	0.1678
Argmin. Corr.	1500
Min. Corr.	0.1504
NSC	1.1282
RSC	1.1022

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	0.4507

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	0.1593
AUC	0.4936
CHANCE divergence	0.2022
Elbow Point	0.0000
JS Distance	0.7812
Synthetic AUC	0.5064
Synthetic Elbow Point	0.3393
Synthetic JS Distance	0.4594