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Report generated at 2020-05-14 11:18:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	120977938	75348014
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115418123	72639776
Mapped(QC-failed)	0	0
% Mapped	95.4000	96.4100
Paired	120977938	75348014
Paired(QC-failed)	0	0
Read1	60488969	37674007
Read1(QC-failed)	0	0
Read2	60488969	37674007
Read2(QC-failed)	0	0
Properly Paired	113775312	70114889
Properly Paired(QC-failed)	0	0
% Properly Paired	94.0500	93.0500
With itself	114919666	71857749
With itself(QC-failed)	0	0
Singletons	498457	782027
Singletons(QC-failed)	0	0
% Singleton	0.4100	1.0400
Diff. Chroms	689985	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	51773718	30082479
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	257911	117823
Paired Opt. Dupes	1322	447
% Dupes/100	0.0050	0.0039

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	51770570	30056490
Distinct Read Pairs	51512672	29938925
One Read Pair	51256119	29821774
Two Read Pairs	255216	116742
NRF = Distinct/Total	0.9950	0.9961
PBC1 = OnePair/Distinct	0.9950	0.9961
PBC2 = OnePair/TwoPair	200.8343	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	103031614	59929312
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103031614	59929312
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	103031614	59929312
Paired(QC-failed)	0	0
Read1	51515807	29964656
Read1(QC-failed)	0	0
Read2	51515807	29964656
Read2(QC-failed)	0	0
Properly Paired	103031614	59929312
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	103031614	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	188731
Np	0
N optimal	188731
N conservative	188731
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.	155
Corr. Est. Fragment Len.	0.1875
Phantom Peak	50
Corr. Phantom Peak	0.1931
Argmin. Corr.	1500
Min. Corr.	0.1780
NSC	1.0530
RSC	0.6259

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	0.2500

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	0.2168
AUC	0.4960
CHANCE divergence	0.1087
Elbow Point	0.0000
JS Distance	0.6994
Synthetic AUC	0.5046
Synthetic Elbow Point	0.1163
Synthetic JS Distance	0.3857