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Report generated at 2019-11-03 17:17:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	130293024	149933526
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	123378151	146624545
Mapped(QC-failed)	0	0
% Mapped	94.6900	97.7900
Paired	130293024	149933526
Paired(QC-failed)	0	0
Read1	65146512	74966763
Read1(QC-failed)	0	0
Read2	65146512	74966763
Read2(QC-failed)	0	0
Properly Paired	119736897	143525972
Properly Paired(QC-failed)	0	0
% Properly Paired	91.9000	95.7300
With itself	121782635	145761822
With itself(QC-failed)	0	0
Singletons	1595516	862723
Singletons(QC-failed)	0	0
% Singleton	1.2200	0.5800
Diff. Chroms	370662	564786
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	42825146	63655918
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	697522	1138162
Paired Opt. Dupes	16411	22681
% Dupes/100	0.0163	0.0179

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42824459	63588650
Distinct Read Pairs	42126943	62452487
One Read Pair	41458563	61334967
Two Read Pairs	648119	1100229
NRF = Distinct/Total	0.9837	0.9821
PBC1 = OnePair/Distinct	0.9841	0.9821
PBC2 = OnePair/TwoPair	63.9675	55.7475

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	84255248	125035512
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	84255248	125035512
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	84255248	125035512
Paired(QC-failed)	0	0
Read1	42127624	62517756
Read1(QC-failed)	0	0
Read2	42127624	62517756
Read2(QC-failed)	0	0
Properly Paired	84255248	125035512
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	84255248	125035512
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	224389
Np	0
N optimal	224389
N conservative	224389
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.	125
Corr. Est. Fragment Len.	0.2159
Phantom Peak	50
Corr. Phantom Peak	0.2670
Argmin. Corr.	1500
Min. Corr.	0.2051
NSC	1.0525
RSC	0.1737

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	0.4276

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	0.1646
AUC	0.4956
CHANCE divergence	0.2092
Elbow Point	0.0000
JS Distance	0.7012
Synthetic AUC	0.5079
Synthetic Elbow Point	0.3316
Synthetic JS Distance	0.4453