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Report generated at 2019-10-13 12:07:59

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	144306080	124377178
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	142011167	122176918
Mapped(QC-failed)	0	0
% Mapped	98.4100	98.2300
Paired	144306080	124377178
Paired(QC-failed)	0	0
Read1	72153040	62188589
Read1(QC-failed)	0	0
Read2	72153040	62188589
Read2(QC-failed)	0	0
Properly Paired	141232584	121113443
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8700	97.3800
With itself	141671719	121685768
With itself(QC-failed)	0	0
Singletons	339448	491150
Singletons(QC-failed)	0	0
% Singleton	0.2400	0.3900
Diff. Chroms	130388	186530
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	64815652	53571906
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	7197222	575059
Paired Opt. Dupes	5828	3236
% Dupes/100	0.1110	0.0107

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	64812494	53150030
Distinct Read Pairs	57615608	52630794
One Read Pair	51119048	52121362
Two Read Pairs	5858977	501851
NRF = Distinct/Total	0.8890	0.9902
PBC1 = OnePair/Distinct	0.8872	0.9903
PBC2 = OnePair/TwoPair	8.7249	103.8582

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	115236860	105993694
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	115236860	105993694
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	115236860	105993694
Paired(QC-failed)	0	0
Read1	57618430	52996847
Read1(QC-failed)	0	0
Read2	57618430	52996847
Read2(QC-failed)	0	0
Properly Paired	115236860	105993694
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	115236860	105993694
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	236643
Np	0
N optimal	236643
N conservative	236643
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.	165
Corr. Est. Fragment Len.	0.1751
Phantom Peak	50
Corr. Phantom Peak	0.1756
Argmin. Corr.	1500
Min. Corr.	0.1733
NSC	1.0101
RSC	0.7867

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	0.3008

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	0.2133
AUC	0.4962
CHANCE divergence	0.1376
Elbow Point	0.0000
JS Distance	0.6401
Synthetic AUC	0.5055
Synthetic Elbow Point	0.2355
Synthetic JS Distance	0.3829