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Report generated at 2020-04-11 00:16:32

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	180758884	163266420
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	172903034	147055862
Mapped(QC-failed)	0	0
% Mapped	95.6500	90.0700
Paired	180758884	163266420
Paired(QC-failed)	0	0
Read1	90379442	81633210
Read1(QC-failed)	0	0
Read2	90379442	81633210
Read2(QC-failed)	0	0
Properly Paired	168581273	131717614
Properly Paired(QC-failed)	0	0
% Properly Paired	93.2600	80.6800
With itself	169358711	140493174
With itself(QC-failed)	0	0
Singletons	3544323	6562688
Singletons(QC-failed)	0	0
% Singleton	1.9600	4.0200
Diff. Chroms	258081	2800249
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	63991072	43256772
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3633984	4012335
Paired Opt. Dupes	28625	298855
% Dupes/100	0.0568	0.0928

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	63974120	42734600
Distinct Read Pairs	60341334	38829854
One Read Pair	56890587	35276734
Two Read Pairs	3277623	3232143
NRF = Distinct/Total	0.9432	0.9086
PBC1 = OnePair/Distinct	0.9428	0.9085
PBC2 = OnePair/TwoPair	17.3573	10.9143

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	120714176	78488874
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	120714176	78488874
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	120714176	78488874
Paired(QC-failed)	0	0
Read1	60357088	39244437
Read1(QC-failed)	0	0
Read2	60357088	39244437
Read2(QC-failed)	0	0
Properly Paired	120714176	78488874
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	120714176	78488874
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	197158
Np	0
N optimal	197158
N conservative	197158
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.	150
Corr. Est. Fragment Len.	0.1871
Phantom Peak	50
Corr. Phantom Peak	0.1898
Argmin. Corr.	1500
Min. Corr.	0.1835
NSC	1.0199
RSC	0.5821

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	0.5136

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	0.1631
AUC	0.4963
CHANCE divergence	0.1207
Elbow Point	0.0000
JS Distance	0.7738
Synthetic AUC	0.4987
Synthetic Elbow Point	0.3530
Synthetic JS Distance	0.4810