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Report generated at 2020-05-10 12:56:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	71321896	56322388
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	65835759	54322392
Mapped(QC-failed)	0	0
% Mapped	92.3100	96.4500
Paired	71321896	56322388
Paired(QC-failed)	0	0
Read1	35660948	28161194
Read1(QC-failed)	0	0
Read2	35660948	28161194
Read2(QC-failed)	0	0
Properly Paired	61247220	50952662
Properly Paired(QC-failed)	0	0
% Properly Paired	85.8700	90.4700
With itself	64343096	53611780
With itself(QC-failed)	0	0
Singletons	1492663	710612
Singletons(QC-failed)	0	0
% Singleton	2.0900	1.2600
Diff. Chroms	1199163	1857685
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	24328918	22368630
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	168737	147561
Paired Opt. Dupes	2078	1794
% Dupes/100	0.0069	0.0066

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24327887	22347851
Distinct Read Pairs	24159158	22200612
One Read Pair	23992105	22054209
Two Read Pairs	165510	145570
NRF = Distinct/Total	0.9931	0.9934
PBC1 = OnePair/Distinct	0.9931	0.9934
PBC2 = OnePair/TwoPair	144.9586	151.5024

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	48320362	44442138
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	48320362	44442138
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	48320362	44442138
Paired(QC-failed)	0	0
Read1	24160181	22221069
Read1(QC-failed)	0	0
Read2	24160181	22221069
Read2(QC-failed)	0	0
Properly Paired	48320362	44442138
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	48320362	44442138
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	76564
Np	0
N optimal	76564
N conservative	76564
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.	240
Corr. Est. Fragment Len.	0.1934
Phantom Peak	50
Corr. Phantom Peak	0.2173
Argmin. Corr.	1500
Min. Corr.	0.1794
NSC	1.0784
RSC	0.3708

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	0.0909

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	0.2037
AUC	0.4941
CHANCE divergence	0.2751
Elbow Point	0.0000
JS Distance	0.6026
Synthetic AUC	0.5078
Synthetic Elbow Point	0.0577
Synthetic JS Distance	0.3289