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Report generated at 2020-07-10 07:32:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	152493968	134911976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	143236301	131561749
Mapped(QC-failed)	0	0
% Mapped	93.9300	97.5200
Paired	152493968	134911976
Paired(QC-failed)	0	0
Read1	76246984	67455988
Read1(QC-failed)	0	0
Read2	76246984	67455988
Read2(QC-failed)	0	0
Properly Paired	141006660	129326590
Properly Paired(QC-failed)	0	0
% Properly Paired	92.4700	95.8600
With itself	142216175	130892791
With itself(QC-failed)	0	0
Singletons	1020126	668958
Singletons(QC-failed)	0	0
% Singleton	0.6700	0.5000
Diff. Chroms	552106	887675
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	60879717	56598486
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	396699	240623
Paired Opt. Dupes	867	1949
% Dupes/100	0.0065	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	60873813	56554856
Distinct Read Pairs	60477146	56314799
One Read Pair	60083656	56075865
Two Read Pairs	390358	237833
NRF = Distinct/Total	0.9935	0.9958
PBC1 = OnePair/Distinct	0.9935	0.9958
PBC2 = OnePair/TwoPair	153.9194	235.7783

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	120966036	112715726
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	120966036	112715726
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	120966036	112715726
Paired(QC-failed)	0	0
Read1	60483018	56357863
Read1(QC-failed)	0	0
Read2	60483018	56357863
Read2(QC-failed)	0	0
Properly Paired	120966036	112715726
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	120966036	112715726
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	130110
Np	0
N optimal	130110
N conservative	130110
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.	145
Corr. Est. Fragment Len.	0.1823
Phantom Peak	50
Corr. Phantom Peak	0.2017
Argmin. Corr.	1500
Min. Corr.	0.1745
NSC	1.0441
RSC	0.2833

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	0.0888

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	0.2817
AUC	0.4963
CHANCE divergence	0.1004
Elbow Point	0.0000
JS Distance	0.5884
Synthetic AUC	0.5054
Synthetic Elbow Point	0.0939
Synthetic JS Distance	0.2786