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Report generated at 2019-11-04 00:43:39

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	186245972	175026970
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	184199427	171819448
Mapped(QC-failed)	0	0
% Mapped	98.9000	98.1700
Paired	186245972	175026970
Paired(QC-failed)	0	0
Read1	93122986	87513485
Read1(QC-failed)	0	0
Read2	93122986	87513485
Read2(QC-failed)	0	0
Properly Paired	181890712	168294620
Properly Paired(QC-failed)	0	0
% Properly Paired	97.6600	96.1500
With itself	183376174	170965028
With itself(QC-failed)	0	0
Singletons	823253	854420
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.4900
Diff. Chroms	446433	1256632
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	82687327	74970360
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2317747	1349605
Paired Opt. Dupes	21407	20203
% Dupes/100	0.0280	0.0180

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	82685841	74828889
Distinct Read Pairs	80368126	73485563
One Read Pair	78094317	72156748
Two Read Pairs	2230797	1315961
NRF = Distinct/Total	0.9720	0.9820
PBC1 = OnePair/Distinct	0.9717	0.9819
PBC2 = OnePair/TwoPair	35.0074	54.8320

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	160739160	147241510
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	160739160	147241510
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	160739160	147241510
Paired(QC-failed)	0	0
Read1	80369580	73620755
Read1(QC-failed)	0	0
Read2	80369580	73620755
Read2(QC-failed)	0	0
Properly Paired	160739160	147241510
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	160739160	147241510
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	224144
Np	0
N optimal	224144
N conservative	224144
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.	155
Corr. Est. Fragment Len.	0.1733
Phantom Peak	50
Corr. Phantom Peak	0.1746
Argmin. Corr.	1500
Min. Corr.	0.1722
NSC	1.0066
RSC	0.4739

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	0.2418

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	0.2572
AUC	0.4968
CHANCE divergence	0.1014
Elbow Point	0.0000
JS Distance	0.5996
Synthetic AUC	0.5051
Synthetic Elbow Point	0.1932
Synthetic JS Distance	0.3239