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Report generated at 2020-07-10 04:12:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	122445058	172997562
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	121372352	170514341
Mapped(QC-failed)	0	0
% Mapped	99.1200	98.5600
Paired	122445058	172997562
Paired(QC-failed)	0	0
Read1	61222529	86498781
Read1(QC-failed)	0	0
Read2	61222529	86498781
Read2(QC-failed)	0	0
Properly Paired	120177238	165526176
Properly Paired(QC-failed)	0	0
% Properly Paired	98.1500	95.6800
With itself	120993035	169780024
With itself(QC-failed)	0	0
Singletons	379317	734317
Singletons(QC-failed)	0	0
% Singleton	0.3100	0.4200
Diff. Chroms	154178	214733
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	55723220	72844563
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	718796	589909
Paired Opt. Dupes	3051	3866
% Dupes/100	0.0129	0.0081

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	55677597	72728950
Distinct Read Pairs	54965527	72170728
One Read Pair	54270928	71649358
Two Read Pairs	679302	508600
NRF = Distinct/Total	0.9872	0.9923
PBC1 = OnePair/Distinct	0.9874	0.9928
PBC2 = OnePair/TwoPair	79.8922	140.8757

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	110008848	144509308
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	110008848	144509308
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	110008848	144509308
Paired(QC-failed)	0	0
Read1	55004424	72254654
Read1(QC-failed)	0	0
Read2	55004424	72254654
Read2(QC-failed)	0	0
Properly Paired	110008848	144509308
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	110008848	144509308
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	249978
Np	0
N optimal	249978
N conservative	249978
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.	135
Corr. Est. Fragment Len.	0.1819
Phantom Peak	45
Corr. Phantom Peak	0.1789
Argmin. Corr.	1500
Min. Corr.	0.1698
NSC	1.0714
RSC	1.3342

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	0.4078

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	0.2158
AUC	0.4961
CHANCE divergence	0.1073
Elbow Point	0.0000
JS Distance	0.7355
Synthetic AUC	0.4991
Synthetic Elbow Point	0.2769
Synthetic JS Distance	0.3887