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Report generated at 2019-10-31 00:55:30

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	100002594	168079694
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97986495	165646880
Mapped(QC-failed)	0	0
% Mapped	97.9800	98.5500
Paired	100002594	168079694
Paired(QC-failed)	0	0
Read1	50001297	84039847
Read1(QC-failed)	0	0
Read2	50001297	84039847
Read2(QC-failed)	0	0
Properly Paired	95975500	159505121
Properly Paired(QC-failed)	0	0
% Properly Paired	95.9700	94.9000
With itself	97380125	164126359
With itself(QC-failed)	0	0
Singletons	606370	1520521
Singletons(QC-failed)	0	0
% Singleton	0.6100	0.9000
Diff. Chroms	959890	2770169
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	41300869	66513677
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3521953	3909802
Paired Opt. Dupes	6491	10372
% Dupes/100	0.0853	0.0588

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	41299934	66496808
Distinct Read Pairs	37778052	62587995
One Read Pair	34497031	58831025
Two Read Pairs	3055679	3612814
NRF = Distinct/Total	0.9147	0.9412
PBC1 = OnePair/Distinct	0.9132	0.9400
PBC2 = OnePair/TwoPair	11.2895	16.2840

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	75557832	125207750
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75557832	125207750
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75557832	125207750
Paired(QC-failed)	0	0
Read1	37778916	62603875
Read1(QC-failed)	0	0
Read2	37778916	62603875
Read2(QC-failed)	0	0
Properly Paired	75557832	125207750
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75557832	125207750
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	140240
Np	0
N optimal	140240
N conservative	140240
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.	155
Corr. Est. Fragment Len.	0.1936
Phantom Peak	50
Corr. Phantom Peak	0.1970
Argmin. Corr.	1500
Min. Corr.	0.1791
NSC	1.0814
RSC	0.8118

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	0.4573

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	0.1837
AUC	0.4943
CHANCE divergence	0.1259
Elbow Point	0.0000
JS Distance	0.8061
Synthetic AUC	0.4996
Synthetic Elbow Point	0.3518
Synthetic JS Distance	0.4464