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Report generated at 2020-06-05 18:36:53

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98652888	124377178
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50025711	122176916
Mapped(QC-failed)	0	0
% Mapped	50.7100	98.2300
Paired	98652888	124377178
Paired(QC-failed)	0	0
Read1	49326444	62188589
Read1(QC-failed)	0	0
Read2	49326444	62188589
Read2(QC-failed)	0	0
Properly Paired	49038478	121113509
Properly Paired(QC-failed)	0	0
% Properly Paired	49.7100	97.3800
With itself	49442726	121685766
With itself(QC-failed)	0	0
Singletons	582985	491150
Singletons(QC-failed)	0	0
% Singleton	0.5900	0.3900
Diff. Chroms	70100	186540
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	19109181	53571782
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6824119	574994
Paired Opt. Dupes	97095	3239
% Dupes/100	0.3571	0.0107

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19101995	53149925
Distinct Read Pairs	12280390	52630751
One Read Pair	7860057	52121382
Two Read Pairs	2851874	501790
NRF = Distinct/Total	0.6429	0.9902
PBC1 = OnePair/Distinct	0.6400	0.9903
PBC2 = OnePair/TwoPair	2.7561	103.8709

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	24570124	105993576
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	24570124	105993576
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	24570124	105993576
Paired(QC-failed)	0	0
Read1	12285062	52996788
Read1(QC-failed)	0	0
Read2	12285062	52996788
Read2(QC-failed)	0	0
Properly Paired	24570124	105993576
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	24570124	105993576
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	81396
Np	0
N optimal	81396
N conservative	81396
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.	120
Corr. Est. Fragment Len.	0.1556
Phantom Peak	50
Corr. Phantom Peak	0.1845
Argmin. Corr.	1500
Min. Corr.	0.1426
NSC	1.0910
RSC	0.3096

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	0.0726

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	0.2354
AUC	0.4918
CHANCE divergence	0.2135
Elbow Point	0.0000
JS Distance	0.5810
Synthetic AUC	0.5125
Synthetic Elbow Point	0.1406
Synthetic JS Distance	0.2888