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Report generated at 2019-11-04 07:49:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	205780008	213968900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	204142286	211195024
Mapped(QC-failed)	0	0
% Mapped	99.2000	98.7000
Paired	205780008	213968900
Paired(QC-failed)	0	0
Read1	102890004	106984450
Read1(QC-failed)	0	0
Read2	102890004	106984450
Read2(QC-failed)	0	0
Properly Paired	201793268	206798914
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0600	96.6500
With itself	203419518	210073494
With itself(QC-failed)	0	0
Singletons	722768	1121530
Singletons(QC-failed)	0	0
% Singleton	0.3500	0.5200
Diff. Chroms	795912	2031909
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	89410491	91477404
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2590999	2315030
Paired Opt. Dupes	43571	43440
% Dupes/100	0.0290	0.0253

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	89410109	91372844
Distinct Read Pairs	86819119	89062444
One Read Pair	84284781	86800060
Two Read Pairs	2478884	2218941
NRF = Distinct/Total	0.9710	0.9747
PBC1 = OnePair/Distinct	0.9708	0.9746
PBC2 = OnePair/TwoPair	34.0011	39.1178

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	173638984	178324748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	173638984	178324748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	173638984	178324748
Paired(QC-failed)	0	0
Read1	86819492	89162374
Read1(QC-failed)	0	0
Read2	86819492	89162374
Read2(QC-failed)	0	0
Properly Paired	173638984	178324748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	173638984	178324748
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	220212
Np	0
N optimal	220212
N conservative	220212
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.	190
Corr. Est. Fragment Len.	0.1747
Phantom Peak	50
Corr. Phantom Peak	0.1776
Argmin. Corr.	1500
Min. Corr.	0.1728
NSC	1.0108
RSC	0.3872

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	0.2806

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	0.2566
AUC	0.4969
CHANCE divergence	0.1199
Elbow Point	0.0000
JS Distance	0.5802
Synthetic AUC	0.5038
Synthetic Elbow Point	0.2127
Synthetic JS Distance	0.3217