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Report generated at 2019-10-12 19:38:53

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	60947142	124377178
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	24160688	122176918
Mapped(QC-failed)	0	0
% Mapped	39.6400	98.2300
Paired	60947142	124377178
Paired(QC-failed)	0	0
Read1	30473571	62188589
Read1(QC-failed)	0	0
Read2	30473571	62188589
Read2(QC-failed)	0	0
Properly Paired	23547720	121113443
Properly Paired(QC-failed)	0	0
% Properly Paired	38.6400	97.3800
With itself	23924828	121685768
With itself(QC-failed)	0	0
Singletons	235860	491150
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.3900
Diff. Chroms	19780	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	10662434	53571906
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4248218	575059
Paired Opt. Dupes	38392	3236
% Dupes/100	0.3984	0.0107

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	10657519	53150030
Distinct Read Pairs	6411331	52630794
One Read Pair	3989485	52121362
Two Read Pairs	1363466	501851
NRF = Distinct/Total	0.6016	0.9902
PBC1 = OnePair/Distinct	0.6223	0.9903
PBC2 = OnePair/TwoPair	2.9260	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	12828432	105993694
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	12828432	105993694
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	12828432	105993694
Paired(QC-failed)	0	0
Read1	6414216	52996847
Read1(QC-failed)	0	0
Read2	6414216	52996847
Read2(QC-failed)	0	0
Properly Paired	12828432	105993694
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	12828432	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	63287
Np	0
N optimal	63287
N conservative	63287
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 (12M)

	rep1
Reads	12201327
Est. Fragment Len.	120
Corr. Est. Fragment Len.	0.1995
Phantom Peak	55
Corr. Phantom Peak	0.1737
Argmin. Corr.	1500
Min. Corr.	0.1021
NSC	1.9545
RSC	1.3593

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	0.4441

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	0.0971
AUC	0.4886
CHANCE divergence	0.5191
Elbow Point	0.0000
JS Distance	0.8224
Synthetic AUC	0.5077
Synthetic Elbow Point	0.4066
Synthetic JS Distance	0.4803