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Report generated at 2020-06-10 10:18:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	64528196	134911976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62460018	131561748
Mapped(QC-failed)	0	0
% Mapped	96.7900	97.5200
Paired	64528196	134911976
Paired(QC-failed)	0	0
Read1	32264098	67455988
Read1(QC-failed)	0	0
Read2	32264098	67455988
Read2(QC-failed)	0	0
Properly Paired	61796226	129326575
Properly Paired(QC-failed)	0	0
% Properly Paired	95.7700	95.8600
With itself	62221246	130892790
With itself(QC-failed)	0	0
Singletons	238772	668958
Singletons(QC-failed)	0	0
% Singleton	0.3700	0.5000
Diff. Chroms	266982	887686
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	28036603	56597685
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	345260	240684
Paired Opt. Dupes	1054	1949
% Dupes/100	0.0123	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28030836	56554078
Distinct Read Pairs	27685653	56313956
One Read Pair	27344626	56074958
Two Read Pairs	336925	237897
NRF = Distinct/Total	0.9877	0.9958
PBC1 = OnePair/Distinct	0.9877	0.9958
PBC2 = OnePair/TwoPair	81.1594	235.7111

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	55382686	112714002
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55382686	112714002
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55382686	112714002
Paired(QC-failed)	0	0
Read1	27691343	56357001
Read1(QC-failed)	0	0
Read2	27691343	56357001
Read2(QC-failed)	0	0
Properly Paired	55382686	112714002
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55382686	112714002
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	35821
Np	0
N optimal	35821
N conservative	35821
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.	200
Corr. Est. Fragment Len.	0.2978
Phantom Peak	50
Corr. Phantom Peak	0.2813
Argmin. Corr.	1500
Min. Corr.	0.1805
NSC	1.6501
RSC	1.1630

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	0.4021

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	0.1750
AUC	0.4945
CHANCE divergence	0.1387
Elbow Point	0.0000
JS Distance	0.7925
Synthetic AUC	0.5036
Synthetic Elbow Point	0.3933
Synthetic JS Distance	0.4876