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Report generated at 2019-10-13 06:02:50

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	97723686	100468200
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	96431911	98722536
Mapped(QC-failed)	0	0
% Mapped	98.6800	98.2600
Paired	97723686	100468200
Paired(QC-failed)	0	0
Read1	48861843	50234100
Read1(QC-failed)	0	0
Read2	48861843	50234100
Read2(QC-failed)	0	0
Properly Paired	95737038	97581946
Properly Paired(QC-failed)	0	0
% Properly Paired	97.9700	97.1300
With itself	96003289	98187762
With itself(QC-failed)	0	0
Singletons	428622	534774
Singletons(QC-failed)	0	0
% Singleton	0.4400	0.5300
Diff. Chroms	69124	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	42066759	42692718
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4213210	481852
Paired Opt. Dupes	9595	6941
% Dupes/100	0.1002	0.0113

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42066049	42649523
Distinct Read Pairs	37852883	42168744
One Read Pair	33999852	41697848
Two Read Pairs	3521318	463478
NRF = Distinct/Total	0.8998	0.9887
PBC1 = OnePair/Distinct	0.8982	0.9888
PBC2 = OnePair/TwoPair	9.6554	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	75707098	84421732
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75707098	84421732
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75707098	84421732
Paired(QC-failed)	0	0
Read1	37853549	42210866
Read1(QC-failed)	0	0
Read2	37853549	42210866
Read2(QC-failed)	0	0
Properly Paired	75707098	84421732
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75707098	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	184245
Np	0
N optimal	184245
N conservative	184245
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.	135
Corr. Est. Fragment Len.	0.1807
Phantom Peak	50
Corr. Phantom Peak	0.1930
Argmin. Corr.	1500
Min. Corr.	0.1720
NSC	1.0504
RSC	0.4139

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	0.1465

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	0.2217
AUC	0.4953
CHANCE divergence	0.2155
Elbow Point	0.0000
JS Distance	0.5921
Synthetic AUC	0.5016
Synthetic Elbow Point	0.1504
Synthetic JS Distance	0.3311