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Report generated at 2020-05-13 19:48:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	92696858	92901862
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	85112545	87995521
Mapped(QC-failed)	0	0
% Mapped	91.8200	94.7200
Paired	92696858	92901862
Paired(QC-failed)	0	0
Read1	46348429	46450931
Read1(QC-failed)	0	0
Read2	46348429	46450931
Read2(QC-failed)	0	0
Properly Paired	80884687	74516594
Properly Paired(QC-failed)	0	0
% Properly Paired	87.2600	80.2100
With itself	82222148	84730641
With itself(QC-failed)	0	0
Singletons	2890397	3264880
Singletons(QC-failed)	0	0
% Singleton	3.1200	3.5100
Diff. Chroms	962813	6656575
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	34452582	28454434
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	546881	260144
Paired Opt. Dupes	1996	1146
% Dupes/100	0.0159	0.0091

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	34449919	28454249
Distinct Read Pairs	33903070	28194105
One Read Pair	33363650	27936016
Two Read Pairs	532086	256046
NRF = Distinct/Total	0.9841	0.9909
PBC1 = OnePair/Distinct	0.9841	0.9908
PBC2 = OnePair/TwoPair	62.7035	109.1055

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	67811402	56388580
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	67811402	56388580
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	67811402	56388580
Paired(QC-failed)	0	0
Read1	33905701	28194290
Read1(QC-failed)	0	0
Read2	33905701	28194290
Read2(QC-failed)	0	0
Properly Paired	67811402	56388580
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	67811402	56388580
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	199973
Np	0
N optimal	199973
N conservative	199973
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.	250
Corr. Est. Fragment Len.	0.2235
Phantom Peak	50
Corr. Phantom Peak	0.2115
Argmin. Corr.	1500
Min. Corr.	0.1989
NSC	1.1238
RSC	1.9507

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	0.4793

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	0.0968
AUC	0.4950
CHANCE divergence	0.4272
Elbow Point	0.0000
JS Distance	0.7836
Synthetic AUC	0.5083
Synthetic Elbow Point	0.1451
Synthetic JS Distance	0.5076