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Report generated at 2020-05-10 19:20:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	123405092	46329162
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112927808	42236466
Mapped(QC-failed)	0	0
% Mapped	91.5100	91.1700
Paired	123405092	46329162
Paired(QC-failed)	0	0
Read1	61702546	23164581
Read1(QC-failed)	0	0
Read2	61702546	23164581
Read2(QC-failed)	0	0
Properly Paired	106277540	32074059
Properly Paired(QC-failed)	0	0
% Properly Paired	86.1200	69.2300
With itself	109590791	40063460
With itself(QC-failed)	0	0
Singletons	3337017	2173006
Singletons(QC-failed)	0	0
% Singleton	2.7000	4.6900
Diff. Chroms	2482138	5498059
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	44740492	11378400
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	435050	199707
Paired Opt. Dupes	2787	452
% Dupes/100	0.0097	0.0176

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44739385	11378350
Distinct Read Pairs	44304347	11178645
One Read Pair	43873030	10981955
Two Read Pairs	427616	193728
NRF = Distinct/Total	0.9903	0.9824
PBC1 = OnePair/Distinct	0.9903	0.9824
PBC2 = OnePair/TwoPair	102.5991	56.6875

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	88610884	22357386
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88610884	22357386
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	88610884	22357386
Paired(QC-failed)	0	0
Read1	44305442	11178693
Read1(QC-failed)	0	0
Read2	44305442	11178693
Read2(QC-failed)	0	0
Properly Paired	88610884	22357386
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	88610884	22357386
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	172076
Np	0
N optimal	172076
N conservative	172076
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.	255
Corr. Est. Fragment Len.	0.2264
Phantom Peak	50
Corr. Phantom Peak	0.2127
Argmin. Corr.	1500
Min. Corr.	0.1988
NSC	1.1388
RSC	1.9813

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	0.4274

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	0.1026
AUC	0.4956
CHANCE divergence	0.3962
Elbow Point	0.0000
JS Distance	0.7714
Synthetic AUC	0.4988
Synthetic Elbow Point	0.1772
Synthetic JS Distance	0.5093