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Report generated at 2020-04-08 17:04:28

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	126080370	67922260
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102242746	66671924
Mapped(QC-failed)	0	0
% Mapped	81.0900	98.1600
Paired	126080370	67922260
Paired(QC-failed)	0	0
Read1	63040185	33961130
Read1(QC-failed)	0	0
Read2	63040185	33961130
Read2(QC-failed)	0	0
Properly Paired	100822355	65974861
Properly Paired(QC-failed)	0	0
% Properly Paired	79.9700	97.1300
With itself	101245187	66190036
With itself(QC-failed)	0	0
Singletons	997559	481888
Singletons(QC-failed)	0	0
% Singleton	0.7900	0.7100
Diff. Chroms	105956	48289
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	44449437	29193042
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2985068	5293802
Paired Opt. Dupes	4375	2781
% Dupes/100	0.0672	0.1813

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44448182	29163692
Distinct Read Pairs	41463216	23873561
One Read Pair	38656840	19715715
Two Read Pairs	2637711	3278552
NRF = Distinct/Total	0.9328	0.8186
PBC1 = OnePair/Distinct	0.9323	0.8258
PBC2 = OnePair/TwoPair	14.6554	6.0135

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	82928738	47798480
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	82928738	47798480
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	82928738	47798480
Paired(QC-failed)	0	0
Read1	41464369	23899240
Read1(QC-failed)	0	0
Read2	41464369	23899240
Read2(QC-failed)	0	0
Properly Paired	82928738	47798480
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	82928738	47798480
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	123535
Np	0
N optimal	123535
N conservative	123535
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.	210
Corr. Est. Fragment Len.	0.1765
Phantom Peak	50
Corr. Phantom Peak	0.1872
Argmin. Corr.	1500
Min. Corr.	0.1701
NSC	1.0373
RSC	0.3714

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	0.1543

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	0.2819
AUC	0.4955
CHANCE divergence	0.1079
Elbow Point	0.0000
JS Distance	0.6144
Synthetic AUC	0.4965
Synthetic Elbow Point	0.0942
Synthetic JS Distance	0.2758