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Report generated at 2019-10-13 08:35:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104306360	100468200
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	101513154	98722536
Mapped(QC-failed)	0	0
% Mapped	97.3200	98.2600
Paired	104306360	100468200
Paired(QC-failed)	0	0
Read1	52153180	50234100
Read1(QC-failed)	0	0
Read2	52153180	50234100
Read2(QC-failed)	0	0
Properly Paired	100404703	97581946
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2600	97.1300
With itself	100942898	98187762
With itself(QC-failed)	0	0
Singletons	570256	534774
Singletons(QC-failed)	0	0
% Singleton	0.5500	0.5300
Diff. Chroms	109118	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	43860661	42692718
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1378994	481852
Paired Opt. Dupes	7780	6941
% Dupes/100	0.0314	0.0113

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43859512	42649523
Distinct Read Pairs	42480548	42168744
One Read Pair	41140767	41697848
Two Read Pairs	1302262	463478
NRF = Distinct/Total	0.9686	0.9887
PBC1 = OnePair/Distinct	0.9685	0.9888
PBC2 = OnePair/TwoPair	31.5918	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	84963334	84421732
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84963334	84421732
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84963334	84421732
Paired(QC-failed)	0	0
Read1	42481667	42210866
Read1(QC-failed)	0	0
Read2	42481667	42210866
Read2(QC-failed)	0	0
Properly Paired	84963334	84421732
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84963334	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	40806
Np	0
N optimal	40806
N conservative	40806
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.	115
Corr. Est. Fragment Len.	0.1748
Phantom Peak	50
Corr. Phantom Peak	0.1864
Argmin. Corr.	1500
Min. Corr.	0.1707
NSC	1.0240
RSC	0.2600

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	0.0249

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	0.3221
AUC	0.4956
CHANCE divergence	0.1030
Elbow Point	0.0000
JS Distance	0.5279
Synthetic AUC	0.5021
Synthetic Elbow Point	0.0382
Synthetic JS Distance	0.2093