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Report generated at 2020-07-09 21:07:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	106084500	135365502
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	105134422	133317923
Mapped(QC-failed)	0	0
% Mapped	99.1000	98.4900
Paired	106084500	135365502
Paired(QC-failed)	0	0
Read1	53042250	67682751
Read1(QC-failed)	0	0
Read2	53042250	67682751
Read2(QC-failed)	0	0
Properly Paired	104455971	128953755
Properly Paired(QC-failed)	0	0
% Properly Paired	98.4600	95.2600
With itself	104849542	132693635
With itself(QC-failed)	0	0
Singletons	284880	624288
Singletons(QC-failed)	0	0
% Singleton	0.2700	0.4600
Diff. Chroms	35650	147654
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	48658397	56839130
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	690094	427070
Paired Opt. Dupes	3647	3620
% Dupes/100	0.0142	0.0075

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48638151	56788289
Distinct Read Pairs	47949651	56369250
One Read Pair	47278863	55975158
Two Read Pairs	655393	386103
NRF = Distinct/Total	0.9858	0.9926
PBC1 = OnePair/Distinct	0.9860	0.9930
PBC2 = OnePair/TwoPair	72.1382	144.9747

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	95936606	112824120
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	95936606	112824120
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	95936606	112824120
Paired(QC-failed)	0	0
Read1	47968303	56412060
Read1(QC-failed)	0	0
Read2	47968303	56412060
Read2(QC-failed)	0	0
Properly Paired	95936606	112824120
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	95936606	112824120
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	224587
Np	0
N optimal	224587
N conservative	224587
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.	150
Corr. Est. Fragment Len.	0.1833
Phantom Peak	45
Corr. Phantom Peak	0.1793
Argmin. Corr.	1500
Min. Corr.	0.1697
NSC	1.0807
RSC	1.4191

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	0.4308

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	0.2052
AUC	0.4959
CHANCE divergence	0.1112
Elbow Point	0.0000
JS Distance	0.7498
Synthetic AUC	0.5068
Synthetic Elbow Point	0.2850
Synthetic JS Distance	0.4059