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Report generated at 2020-06-05 08:16:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	68320974	55795332
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66218208	53857089
Mapped(QC-failed)	0	0
% Mapped	96.9200	96.5300
Paired	68320974	55795332
Paired(QC-failed)	0	0
Read1	34160487	27897666
Read1(QC-failed)	0	0
Read2	34160487	27897666
Read2(QC-failed)	0	0
Properly Paired	64630084	52296480
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6000	93.7300
With itself	64842964	52480399
With itself(QC-failed)	0	0
Singletons	1375244	1376690
Singletons(QC-failed)	0	0
% Singleton	2.0100	2.4700
Diff. Chroms	44777	46059
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	28722728	22626428
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3547064	274417
Paired Opt. Dupes	1723	1375
% Dupes/100	0.1235	0.0121

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28722382	22613174
Distinct Read Pairs	25175362	22338978
One Read Pair	22071829	22067977
Two Read Pairs	2712862	267891
NRF = Distinct/Total	0.8765	0.9879
PBC1 = OnePair/Distinct	0.8767	0.9879
PBC2 = OnePair/TwoPair	8.1360	82.3767

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	50351328	44704022
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50351328	44704022
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	50351328	44704022
Paired(QC-failed)	0	0
Read1	25175664	22352011
Read1(QC-failed)	0	0
Read2	25175664	22352011
Read2(QC-failed)	0	0
Properly Paired	50351328	44704022
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	50351328	44704022
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	26652
Np	0
N optimal	26652
N conservative	26652
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.	210
Corr. Est. Fragment Len.	0.1680
Phantom Peak	50
Corr. Phantom Peak	0.1722
Argmin. Corr.	1500
Min. Corr.	0.1612
NSC	1.0420
RSC	0.6182

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	0.0346

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	0.3069
AUC	0.4943
CHANCE divergence	0.1141
Elbow Point	0.0000
JS Distance	0.5378
Synthetic AUC	0.4957
Synthetic Elbow Point	0.0474
Synthetic JS Distance	0.2263