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Report generated at 2020-05-09 14:34:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	81696518	55171578
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49160997	47068627
Mapped(QC-failed)	0	0
% Mapped	60.1800	85.3100
Paired	81696518	55171578
Paired(QC-failed)	0	0
Read1	40848259	27585789
Read1(QC-failed)	0	0
Read2	40848259	27585789
Read2(QC-failed)	0	0
Properly Paired	44878457	35348053
Properly Paired(QC-failed)	0	0
% Properly Paired	54.9300	64.0700
With itself	46503241	44252810
With itself(QC-failed)	0	0
Singletons	2657756	2815817
Singletons(QC-failed)	0	0
% Singleton	3.2500	5.1000
Diff. Chroms	1043395	5846948
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	19239842	12505350
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	763058	404711
Paired Opt. Dupes	2415	2139
% Dupes/100	0.0397	0.0324

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	19223274	12502680
Distinct Read Pairs	18460863	12098062
One Read Pair	17723918	11705353
Two Read Pairs	712227	381354
NRF = Distinct/Total	0.9603	0.9676
PBC1 = OnePair/Distinct	0.9601	0.9675
PBC2 = OnePair/TwoPair	24.8852	30.6942

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	36953568	24201278
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	36953568	24201278
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	36953568	24201278
Paired(QC-failed)	0	0
Read1	18476784	12100639
Read1(QC-failed)	0	0
Read2	18476784	12100639
Read2(QC-failed)	0	0
Properly Paired	36953568	24201278
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	36953568	24201278
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	24510
Np	0
N optimal	24510
N conservative	24510
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.	280
Corr. Est. Fragment Len.	0.3001
Phantom Peak	50
Corr. Phantom Peak	0.2825
Argmin. Corr.	1500
Min. Corr.	0.1748
NSC	1.7166
RSC	1.1637

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	0.3923

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	0.1233
AUC	0.4932
CHANCE divergence	0.2858
Elbow Point	0.0000
JS Distance	0.7721
Synthetic AUC	0.5111
Synthetic Elbow Point	0.3499
Synthetic JS Distance	0.5211