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Report generated at 2019-10-13 05:54:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	106088890	100468200
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	103220452	98722536
Mapped(QC-failed)	0	0
% Mapped	97.3000	98.2600
Paired	106088890	100468200
Paired(QC-failed)	0	0
Read1	53044445	50234100
Read1(QC-failed)	0	0
Read2	53044445	50234100
Read2(QC-failed)	0	0
Properly Paired	102418014	97581946
Properly Paired(QC-failed)	0	0
% Properly Paired	96.5400	97.1300
With itself	102709992	98187762
With itself(QC-failed)	0	0
Singletons	510460	534774
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5300
Diff. Chroms	58209	175930
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	45223092	42692718
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	20203289	481852
Paired Opt. Dupes	9418	6941
% Dupes/100	0.4467	0.0113

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45220524	42649523
Distinct Read Pairs	25018364	42168744
One Read Pair	13111224	41697848
Two Read Pairs	6747416	463478
NRF = Distinct/Total	0.5533	0.9887
PBC1 = OnePair/Distinct	0.5241	0.9888
PBC2 = OnePair/TwoPair	1.9431	89.9673

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	50039606	84421732
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50039606	84421732
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	50039606	84421732
Paired(QC-failed)	0	0
Read1	25019803	42210866
Read1(QC-failed)	0	0
Read2	25019803	42210866
Read2(QC-failed)	0	0
Properly Paired	50039606	84421732
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	50039606	84421732
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	74281
Np	0
N optimal	74281
N conservative	74281
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.	150
Corr. Est. Fragment Len.	0.1731
Phantom Peak	50
Corr. Phantom Peak	0.1752
Argmin. Corr.	1500
Min. Corr.	0.1504
NSC	1.1506
RSC	0.9134

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	0.1802

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	0.2317
AUC	0.4942
CHANCE divergence	0.1609
Elbow Point	0.0000
JS Distance	0.6357
Synthetic AUC	0.5040
Synthetic Elbow Point	0.2042
Synthetic JS Distance	0.3444