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Report generated at 2020-07-15 11:47:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	122955630	153209202
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112105379	149479079
Mapped(QC-failed)	0	0
% Mapped	91.1800	97.5700
Paired	122955630	153209202
Paired(QC-failed)	0	0
Read1	61477815	76604601
Read1(QC-failed)	0	0
Read2	61477815	76604601
Read2(QC-failed)	0	0
Properly Paired	110427084	147025154
Properly Paired(QC-failed)	0	0
% Properly Paired	89.8100	95.9600
With itself	111380580	148752334
With itself(QC-failed)	0	0
Singletons	724799	726745
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.4700
Diff. Chroms	515880	985904
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	48993418	64022479
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	272791	238123
Paired Opt. Dupes	1867	1074
% Dupes/100	0.0056	0.0037

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48983393	63951647
Distinct Read Pairs	48710686	63714783
One Read Pair	48439541	63480345
Two Read Pairs	269608	232360
NRF = Distinct/Total	0.9944	0.9963
PBC1 = OnePair/Distinct	0.9944	0.9963
PBC2 = OnePair/TwoPair	179.6666	273.1982

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	97441254	127568712
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97441254	127568712
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	97441254	127568712
Paired(QC-failed)	0	0
Read1	48720627	63784356
Read1(QC-failed)	0	0
Read2	48720627	63784356
Read2(QC-failed)	0	0
Properly Paired	97441254	127568712
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	97441254	127568712
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	207358
Np	0
N optimal	207358
N conservative	207358
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.	130
Corr. Est. Fragment Len.	0.1940
Phantom Peak	50
Corr. Phantom Peak	0.2100
Argmin. Corr.	1500
Min. Corr.	0.1837
NSC	1.0561
RSC	0.3932

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	0.3773

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	0.2074
AUC	0.4959
CHANCE divergence	0.1099
Elbow Point	0.0000
JS Distance	0.7370
Synthetic AUC	0.5024
Synthetic Elbow Point	0.2593
Synthetic JS Distance	0.4036