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Report generated at 2019-10-12 22:16:11

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	77228890	81954026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	74600838	79524456
Mapped(QC-failed)	0	0
% Mapped	96.6000	97.0400
Paired	77228890	81954026
Paired(QC-failed)	0	0
Read1	38614445	40977013
Read1(QC-failed)	0	0
Read2	38614445	40977013
Read2(QC-failed)	0	0
Properly Paired	72926737	77093830
Properly Paired(QC-failed)	0	0
% Properly Paired	94.4300	94.0700
With itself	74018850	79098584
With itself(QC-failed)	0	0
Singletons	581988	425872
Singletons(QC-failed)	0	0
% Singleton	0.7500	0.5200
Diff. Chroms	457096	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	30176172	34184517
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	440117	147561
Paired Opt. Dupes	7741	4430
% Dupes/100	0.0146	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30175699	34160894
Distinct Read Pairs	29735590	34013583
One Read Pair	29303938	33872187
Two Read Pairs	424418	138075
NRF = Distinct/Total	0.9854	0.9957
PBC1 = OnePair/Distinct	0.9855	0.9958
PBC2 = OnePair/TwoPair	69.0450	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	59472110	68073912
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	59472110	68073912
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	59472110	68073912
Paired(QC-failed)	0	0
Read1	29736055	34036956
Read1(QC-failed)	0	0
Read2	29736055	34036956
Read2(QC-failed)	0	0
Properly Paired	59472110	68073912
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	59472110	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	66719
Np	0
N optimal	66719
N conservative	66719
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.	120
Corr. Est. Fragment Len.	0.1850
Phantom Peak	50
Corr. Phantom Peak	0.2146
Argmin. Corr.	1500
Min. Corr.	0.1786
NSC	1.0359
RSC	0.1786

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	0.0469

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	0.2927
AUC	0.4947
CHANCE divergence	0.1107
Elbow Point	0.0000
JS Distance	0.5591
Synthetic AUC	0.5071
Synthetic Elbow Point	0.0753
Synthetic JS Distance	0.2521