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Report generated at 2020-05-18 16:09:38

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	164446868	91058302
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	156808522	88858777
Mapped(QC-failed)	0	0
% Mapped	95.3600	97.5800
Paired	164446868	91058302
Paired(QC-failed)	0	0
Read1	82223434	45529151
Read1(QC-failed)	0	0
Read2	82223434	45529151
Read2(QC-failed)	0	0
Properly Paired	155093625	87463672
Properly Paired(QC-failed)	0	0
% Properly Paired	94.3100	96.0500
With itself	156113587	88414762
With itself(QC-failed)	0	0
Singletons	694935	444015
Singletons(QC-failed)	0	0
% Singleton	0.4200	0.4900
Diff. Chroms	422768	473257
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	68214373	38226012
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	857828	140477
Paired Opt. Dupes	2271	1407
% Dupes/100	0.0126	0.0037

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	68197613	38152882
Distinct Read Pairs	67340037	38013834
One Read Pair	66494030	37875216
Two Read Pairs	834599	138191
NRF = Distinct/Total	0.9874	0.9964
PBC1 = OnePair/Distinct	0.9874	0.9964
PBC2 = OnePair/TwoPair	79.6718	274.0787

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	134713090	76171070
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	134713090	76171070
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	134713090	76171070
Paired(QC-failed)	0	0
Read1	67356545	38085535
Read1(QC-failed)	0	0
Read2	67356545	38085535
Read2(QC-failed)	0	0
Properly Paired	134713090	76171070
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	134713090	76171070
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	258752
Np	0
N optimal	258752
N conservative	258752
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.	155
Corr. Est. Fragment Len.	0.1880
Phantom Peak	50
Corr. Phantom Peak	0.1955
Argmin. Corr.	1500
Min. Corr.	0.1819
NSC	1.0339
RSC	0.4527

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	0.2182

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	0.2293
AUC	0.4965
CHANCE divergence	0.1078
Elbow Point	0.0000
JS Distance	0.6526
Synthetic AUC	0.5057
Synthetic Elbow Point	0.1513
Synthetic JS Distance	0.3655