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Report generated at 2020-05-27 00:16:05

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	173260846	192176210
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	171163666	189111270
Mapped(QC-failed)	0	0
% Mapped	98.7900	98.4100
Paired	173260846	192176210
Paired(QC-failed)	0	0
Read1	86630423	96088105
Read1(QC-failed)	0	0
Read2	86630423	96088105
Read2(QC-failed)	0	0
Properly Paired	169931819	185500997
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0800	96.5300
With itself	170285647	188039219
With itself(QC-failed)	0	0
Singletons	878019	1072051
Singletons(QC-failed)	0	0
% Singleton	0.5100	0.5600
Diff. Chroms	64300	189715
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	76296299	81981512
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2739382	827169
Paired Opt. Dupes	5608	5791
% Dupes/100	0.0359	0.0101

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	76284857	81951811
Distinct Read Pairs	73546127	81129436
One Read Pair	70905898	80347882
Two Read Pairs	2549167	763850
NRF = Distinct/Total	0.9641	0.9900
PBC1 = OnePair/Distinct	0.9641	0.9904
PBC2 = OnePair/TwoPair	27.8153	105.1880

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	147113834	162308686
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	147113834	162308686
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	147113834	162308686
Paired(QC-failed)	0	0
Read1	73556917	81154343
Read1(QC-failed)	0	0
Read2	73556917	81154343
Read2(QC-failed)	0	0
Properly Paired	147113834	162308686
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	147113834	162308686
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	212626
Np	0
N optimal	212626
N conservative	212626
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.	145
Corr. Est. Fragment Len.	0.1787
Phantom Peak	50
Corr. Phantom Peak	0.1802
Argmin. Corr.	1500
Min. Corr.	0.1724
NSC	1.0365
RSC	0.8107

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	0.2754

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	0.2372
AUC	0.4966
CHANCE divergence	0.0980
Elbow Point	0.0000
JS Distance	0.6489
Synthetic AUC	0.4982
Synthetic Elbow Point	0.1900
Synthetic JS Distance	0.3554