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Report generated at 2020-04-11 04:25:02

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	193880434	163266420
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	180791149	147055862
Mapped(QC-failed)	0	0
% Mapped	93.2500	90.0700
Paired	193880434	163266420
Paired(QC-failed)	0	0
Read1	96940217	81633210
Read1(QC-failed)	0	0
Read2	96940217	81633210
Read2(QC-failed)	0	0
Properly Paired	173888441	131717614
Properly Paired(QC-failed)	0	0
% Properly Paired	89.6900	80.6800
With itself	175449745	140493174
With itself(QC-failed)	0	0
Singletons	5341404	6562688
Singletons(QC-failed)	0	0
% Singleton	2.7500	4.0200
Diff. Chroms	387669	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	61439193	43256772
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2595213	4012335
Paired Opt. Dupes	28450	298855
% Dupes/100	0.0422	0.0928

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	61419410	42734600
Distinct Read Pairs	58825187	38829854
One Read Pair	56326087	35276734
Two Read Pairs	2408314	3232143
NRF = Distinct/Total	0.9578	0.9086
PBC1 = OnePair/Distinct	0.9575	0.9085
PBC2 = OnePair/TwoPair	23.3882	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	117687960	78488874
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117687960	78488874
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	117687960	78488874
Paired(QC-failed)	0	0
Read1	58843980	39244437
Read1(QC-failed)	0	0
Read2	58843980	39244437
Read2(QC-failed)	0	0
Properly Paired	117687960	78488874
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	117687960	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	257180
Np	0
N optimal	257180
N conservative	257180
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.	110
Corr. Est. Fragment Len.	0.1923
Phantom Peak	50
Corr. Phantom Peak	0.2187
Argmin. Corr.	1500
Min. Corr.	0.1862
NSC	1.0328
RSC	0.1874

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	0.2600

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	0.1909
AUC	0.4963
CHANCE divergence	0.1331
Elbow Point	0.0000
JS Distance	0.6758
Synthetic AUC	0.5017
Synthetic Elbow Point	0.2833
Synthetic JS Distance	0.4304