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Report generated at 2019-10-30 13:15:37

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65331084	143714130
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62909521	141651275
Mapped(QC-failed)	0	0
% Mapped	96.2900	98.5600
Paired	65331084	143714130
Paired(QC-failed)	0	0
Read1	32665542	71857065
Read1(QC-failed)	0	0
Read2	32665542	71857065
Read2(QC-failed)	0	0
Properly Paired	61807331	136021403
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6100	94.6500
With itself	62394240	140589137
With itself(QC-failed)	0	0
Singletons	515281	1062138
Singletons(QC-failed)	0	0
% Singleton	0.7900	0.7400
Diff. Chroms	401073	3177801
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	27555707	56070460
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	5007609	6270525
Paired Opt. Dupes	26677	24403
% Dupes/100	0.1817	0.1118

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27552596	55969749
Distinct Read Pairs	22545519	49713031
One Read Pair	18315957	44051001
Two Read Pairs	3559833	5120262
NRF = Distinct/Total	0.8183	0.8882
PBC1 = OnePair/Distinct	0.8124	0.8861
PBC2 = OnePair/TwoPair	5.1452	8.6033

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	45096196	99599870
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45096196	99599870
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45096196	99599870
Paired(QC-failed)	0	0
Read1	22548098	49799935
Read1(QC-failed)	0	0
Read2	22548098	49799935
Read2(QC-failed)	0	0
Properly Paired	45096196	99599870
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45096196	99599870
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	188603
Np	0
N optimal	188603
N conservative	188603
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.	190
Corr. Est. Fragment Len.	0.1772
Phantom Peak	50
Corr. Phantom Peak	0.1750
Argmin. Corr.	1500
Min. Corr.	0.1638
NSC	1.0815
RSC	1.1943

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	0.4578

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	0.1404
AUC	0.4926
CHANCE divergence	0.2770
Elbow Point	0.0000
JS Distance	0.7486
Synthetic AUC	0.4981
Synthetic Elbow Point	0.3115
Synthetic JS Distance	0.4564