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Report generated at 2020-05-14 10:57:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	103842586	75348014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95164580	72639776
Mapped(QC-failed)	0	0
% Mapped	91.6400	96.4100
Paired	103842586	75348014
Paired(QC-failed)	0	0
Read1	51921293	37674007
Read1(QC-failed)	0	0
Read2	51921293	37674007
Read2(QC-failed)	0	0
Properly Paired	93102044	70114889
Properly Paired(QC-failed)	0	0
% Properly Paired	89.6600	93.0500
With itself	94514468	71857749
With itself(QC-failed)	0	0
Singletons	650112	782027
Singletons(QC-failed)	0	0
% Singleton	0.6300	1.0400
Diff. Chroms	816070	1077494
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	40801908	30082479
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	250730	117823
Paired Opt. Dupes	1520	447
% Dupes/100	0.0061	0.0039

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	40798784	30056490
Distinct Read Pairs	40548075	29938925
One Read Pair	40299275	29821774
Two Read Pairs	246916	116742
NRF = Distinct/Total	0.9939	0.9961
PBC1 = OnePair/Distinct	0.9939	0.9961
PBC2 = OnePair/TwoPair	163.2105	255.4503

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	81102356	59929312
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	81102356	59929312
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	81102356	59929312
Paired(QC-failed)	0	0
Read1	40551178	29964656
Read1(QC-failed)	0	0
Read2	40551178	29964656
Read2(QC-failed)	0	0
Properly Paired	81102356	59929312
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	81102356	59929312
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	193078
Np	0
N optimal	193078
N conservative	193078
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.	0.1940
Phantom Peak	50
Corr. Phantom Peak	0.2093
Argmin. Corr.	1500
Min. Corr.	0.1832
NSC	1.0588
RSC	0.4139

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	0.2701

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	0.2126
AUC	0.4955
CHANCE divergence	0.1145
Elbow Point	0.0000
JS Distance	0.7080
Synthetic AUC	0.5003
Synthetic Elbow Point	0.1332
Synthetic JS Distance	0.3912