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Report generated at 2019-10-31 07:37:00

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	207021200	168079694
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	203737747	165646880
Mapped(QC-failed)	0	0
% Mapped	98.4100	98.5500
Paired	207021200	168079694
Paired(QC-failed)	0	0
Read1	103510600	84039847
Read1(QC-failed)	0	0
Read2	103510600	84039847
Read2(QC-failed)	0	0
Properly Paired	199670751	159505121
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4500	94.9000
With itself	202404036	164126359
With itself(QC-failed)	0	0
Singletons	1333711	1520521
Singletons(QC-failed)	0	0
% Singleton	0.6400	0.9000
Diff. Chroms	1696661	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	82977191	66513677
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	9081765	3909802
Paired Opt. Dupes	15877	10372
% Dupes/100	0.1094	0.0588

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	82976283	66496808
Distinct Read Pairs	73894597	62587995
One Read Pair	65643506	58831025
Two Read Pairs	7489251	3612814
NRF = Distinct/Total	0.8906	0.9412
PBC1 = OnePair/Distinct	0.8883	0.9400
PBC2 = OnePair/TwoPair	8.7650	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	147790852	125207750
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	147790852	125207750
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	147790852	125207750
Paired(QC-failed)	0	0
Read1	73895426	62603875
Read1(QC-failed)	0	0
Read2	73895426	62603875
Read2(QC-failed)	0	0
Properly Paired	147790852	125207750
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	147790852	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	197491
Np	0
N optimal	197491
N conservative	197491
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.	145
Corr. Est. Fragment Len.	0.1833
Phantom Peak	50
Corr. Phantom Peak	0.1899
Argmin. Corr.	1500
Min. Corr.	0.1784
NSC	1.0274
RSC	0.4240

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	0.2304

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	0.2473
AUC	0.4959
CHANCE divergence	0.1065
Elbow Point	0.0000
JS Distance	0.6247
Synthetic AUC	0.4985
Synthetic Elbow Point	0.2065
Synthetic JS Distance	0.3381