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Report generated at 2019-10-13 08:28:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	104980796	100468200
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	100312176	98722536
Mapped(QC-failed)	0	0
% Mapped	95.5500	98.2600
Paired	104980796	100468200
Paired(QC-failed)	0	0
Read1	52490398	50234100
Read1(QC-failed)	0	0
Read2	52490398	50234100
Read2(QC-failed)	0	0
Properly Paired	99383294	97581946
Properly Paired(QC-failed)	0	0
% Properly Paired	94.6700	97.1300
With itself	99754542	98187762
With itself(QC-failed)	0	0
Singletons	557634	534774
Singletons(QC-failed)	0	0
% Singleton	0.5300	0.5300
Diff. Chroms	121884	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	43436247	42692718
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1058426	481852
Paired Opt. Dupes	8764	6941
% Dupes/100	0.0244	0.0113

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	43435056	42649523
Distinct Read Pairs	42376653	42168744
One Read Pair	41341851	41697848
Two Read Pairs	1012093	463478
NRF = Distinct/Total	0.9756	0.9887
PBC1 = OnePair/Distinct	0.9756	0.9888
PBC2 = OnePair/TwoPair	40.8479	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	84755642	84421732
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84755642	84421732
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84755642	84421732
Paired(QC-failed)	0	0
Read1	42377821	42210866
Read1(QC-failed)	0	0
Read2	42377821	42210866
Read2(QC-failed)	0	0
Properly Paired	84755642	84421732
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84755642	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	111014
Np	0
N optimal	111014
N conservative	111014
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.	120
Corr. Est. Fragment Len.	0.1759
Phantom Peak	50
Corr. Phantom Peak	0.1864
Argmin. Corr.	1500
Min. Corr.	0.1723
NSC	1.0208
RSC	0.2529

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	0.0880

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	0.2924
AUC	0.4956
CHANCE divergence	0.1042
Elbow Point	0.0000
JS Distance	0.5946
Synthetic AUC	0.5048
Synthetic Elbow Point	0.0894
Synthetic JS Distance	0.2570