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Report generated at 2019-10-13 00:59:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104784550	81954026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100939132	79524456
Mapped(QC-failed)	0	0
% Mapped	96.3300	97.0400
Paired	104784550	81954026
Paired(QC-failed)	0	0
Read1	52392275	40977013
Read1(QC-failed)	0	0
Read2	52392275	40977013
Read2(QC-failed)	0	0
Properly Paired	100091782	77093830
Properly Paired(QC-failed)	0	0
% Properly Paired	95.5200	94.0700
With itself	100540715	79098584
With itself(QC-failed)	0	0
Singletons	398417	425872
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.5200
Diff. Chroms	117886	1402744
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	45034320	34184517
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7310251	147561
Paired Opt. Dupes	8620	4430
% Dupes/100	0.1623	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45033236	34160894
Distinct Read Pairs	37723171	34013583
One Read Pair	31690647	33872187
Two Read Pairs	4980860	138075
NRF = Distinct/Total	0.8377	0.9957
PBC1 = OnePair/Distinct	0.8401	0.9958
PBC2 = OnePair/TwoPair	6.3625	245.3173

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	75448138	68073912
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75448138	68073912
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75448138	68073912
Paired(QC-failed)	0	0
Read1	37724069	34036956
Read1(QC-failed)	0	0
Read2	37724069	34036956
Read2(QC-failed)	0	0
Properly Paired	75448138	68073912
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75448138	68073912
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	204372
Np	0
N optimal	204372
N conservative	204372
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.	130
Corr. Est. Fragment Len.	0.1715
Phantom Peak	50
Corr. Phantom Peak	0.1783
Argmin. Corr.	1500
Min. Corr.	0.1654
NSC	1.0373
RSC	0.4757

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	0.2865

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	0.2355
AUC	0.4953
CHANCE divergence	0.1117
Elbow Point	0.0000
JS Distance	0.7067
Synthetic AUC	0.5047
Synthetic Elbow Point	0.2066
Synthetic JS Distance	0.3518