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Report generated at 2019-10-31 07:50:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	149010498	239432188
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	136406092	231429253
Mapped(QC-failed)	0	0
% Mapped	91.5400	96.6600
Paired	149010498	239432188
Paired(QC-failed)	0	0
Read1	74505249	119716094
Read1(QC-failed)	0	0
Read2	74505249	119716094
Read2(QC-failed)	0	0
Properly Paired	134362363	226374121
Properly Paired(QC-failed)	0	0
% Properly Paired	90.1700	94.5500
With itself	135158956	229579189
With itself(QC-failed)	0	0
Singletons	1247136	1850064
Singletons(QC-failed)	0	0
% Singleton	0.8400	0.7700
Diff. Chroms	479754	2056124
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	58104358	93939937
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	11804874	11899048
Paired Opt. Dupes	27006	28578
% Dupes/100	0.2032	0.1267

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58103516	93919009
Distinct Read Pairs	46298804	82022723
One Read Pair	36555802	71424617
Two Read Pairs	8002381	9428354
NRF = Distinct/Total	0.7968	0.8733
PBC1 = OnePair/Distinct	0.7896	0.8708
PBC2 = OnePair/TwoPair	4.5681	7.5755

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	92598968	164081778
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	92598968	164081778
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	92598968	164081778
Paired(QC-failed)	0	0
Read1	46299484	82040889
Read1(QC-failed)	0	0
Read2	46299484	82040889
Read2(QC-failed)	0	0
Properly Paired	92598968	164081778
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	92598968	164081778
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	101612
Np	0
N optimal	101612
N conservative	101612
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.	220
Corr. Est. Fragment Len.	0.1944
Phantom Peak	50
Corr. Phantom Peak	0.1957
Argmin. Corr.	1500
Min. Corr.	0.1808
NSC	1.0750
RSC	0.9107

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	0.5112

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	0.1717
AUC	0.4948
CHANCE divergence	0.1189
Elbow Point	0.0000
JS Distance	0.8242
Synthetic AUC	0.4972
Synthetic Elbow Point	0.3911
Synthetic JS Distance	0.4736