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Report generated at 2020-05-14 05:09:28

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63979166	74438840
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59841202	70461728
Mapped(QC-failed)	0	0
% Mapped	93.5300	94.6600
Paired	63979166	74438840
Paired(QC-failed)	0	0
Read1	31989583	37219420
Read1(QC-failed)	0	0
Read2	31989583	37219420
Read2(QC-failed)	0	0
Properly Paired	57249370	63045742
Properly Paired(QC-failed)	0	0
% Properly Paired	89.4800	84.6900
With itself	58091339	67777268
With itself(QC-failed)	0	0
Singletons	1749863	2684460
Singletons(QC-failed)	0	0
% Singleton	2.7400	3.6100
Diff. Chroms	565538	2894050
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	24516870	25565862
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	281958	413905
Paired Opt. Dupes	1508	1303
% Dupes/100	0.0115	0.0162

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24516320	25565508
Distinct Read Pairs	24234367	25151609
One Read Pair	23955180	24743478
Two Read Pairs	276443	402445
NRF = Distinct/Total	0.9885	0.9838
PBC1 = OnePair/Distinct	0.9885	0.9838
PBC2 = OnePair/TwoPair	86.6550	61.4829

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	48469824	50303914
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48469824	50303914
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	48469824	50303914
Paired(QC-failed)	0	0
Read1	24234912	25151957
Read1(QC-failed)	0	0
Read2	24234912	25151957
Read2(QC-failed)	0	0
Properly Paired	48469824	50303914
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	48469824	50303914
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	146532
Np	0
N optimal	146532
N conservative	146532
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.	250
Corr. Est. Fragment Len.	0.2123
Phantom Peak	50
Corr. Phantom Peak	0.2041
Argmin. Corr.	1500
Min. Corr.	0.1942
NSC	1.0933
RSC	1.8273

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	0.3986

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	0.1181
AUC	0.4941
CHANCE divergence	0.4002
Elbow Point	0.0000
JS Distance	0.7378
Synthetic AUC	0.5006
Synthetic Elbow Point	0.1970
Synthetic JS Distance	0.4571