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Report generated at 2020-05-13 15:16:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	75793208	92901862
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	71113610	87995521
Mapped(QC-failed)	0	0
% Mapped	93.8300	94.7200
Paired	75793208	92901862
Paired(QC-failed)	0	0
Read1	37896604	46450931
Read1(QC-failed)	0	0
Read2	37896604	46450931
Read2(QC-failed)	0	0
Properly Paired	68115743	74516594
Properly Paired(QC-failed)	0	0
% Properly Paired	89.8700	80.2100
With itself	69358675	84730641
With itself(QC-failed)	0	0
Singletons	1754935	3264880
Singletons(QC-failed)	0	0
% Singleton	2.3200	3.5100
Diff. Chroms	811198	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	28591442	28454434
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	595262	260144
Paired Opt. Dupes	1586	1146
% Dupes/100	0.0208	0.0091

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	28589924	28454249
Distinct Read Pairs	27994690	28194105
One Read Pair	27409717	27936016
Two Read Pairs	574871	256046
NRF = Distinct/Total	0.9792	0.9909
PBC1 = OnePair/Distinct	0.9791	0.9908
PBC2 = OnePair/TwoPair	47.6798	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	55992360	56388580
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55992360	56388580
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55992360	56388580
Paired(QC-failed)	0	0
Read1	27996180	28194290
Read1(QC-failed)	0	0
Read2	27996180	28194290
Read2(QC-failed)	0	0
Properly Paired	55992360	56388580
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55992360	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	179560
Np	0
N optimal	179560
N conservative	179560
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.	255
Corr. Est. Fragment Len.	0.2298
Phantom Peak	50
Corr. Phantom Peak	0.2188
Argmin. Corr.	1500
Min. Corr.	0.1977
NSC	1.1624
RSC	1.5255

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	0.3548

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	0.1060
AUC	0.4945
CHANCE divergence	0.4313
Elbow Point	0.0000
JS Distance	0.7506
Synthetic AUC	0.5079
Synthetic Elbow Point	0.1065
Synthetic JS Distance	0.4778