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Report generated at 2020-05-13 04:38:43

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	44728752	44822058
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39542694	42270277
Mapped(QC-failed)	0	0
% Mapped	88.4100	94.3100
Paired	44728752	44822058
Paired(QC-failed)	0	0
Read1	22364376	22411029
Read1(QC-failed)	0	0
Read2	22364376	22411029
Read2(QC-failed)	0	0
Properly Paired	37001986	39106937
Properly Paired(QC-failed)	0	0
% Properly Paired	82.7300	87.2500
With itself	38425094	41498214
With itself(QC-failed)	0	0
Singletons	1117600	772063
Singletons(QC-failed)	0	0
% Singleton	2.5000	1.7200
Diff. Chroms	617815	1698756
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	15439240	17000414
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	244404	184749
Paired Opt. Dupes	1433	1571
% Dupes/100	0.0158	0.0109

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	15438928	16997550
Distinct Read Pairs	15194528	16812850
One Read Pair	14953428	16629884
Two Read Pairs	237829	181248
NRF = Distinct/Total	0.9842	0.9891
PBC1 = OnePair/Distinct	0.9841	0.9891
PBC2 = OnePair/TwoPair	62.8747	91.7521

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	30389672	33631330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	30389672	33631330
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	30389672	33631330
Paired(QC-failed)	0	0
Read1	15194836	16815665
Read1(QC-failed)	0	0
Read2	15194836	16815665
Read2(QC-failed)	0	0
Properly Paired	30389672	33631330
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	30389672	33631330
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	90373
Np	0
N optimal	90373
N conservative	90373
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.	285
Corr. Est. Fragment Len.	0.1994
Phantom Peak	50
Corr. Phantom Peak	0.2051
Argmin. Corr.	1500
Min. Corr.	0.1763
NSC	1.1312
RSC	0.8041

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	0.1534

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	0.1611
AUC	0.4926
CHANCE divergence	0.3901
Elbow Point	0.0000
JS Distance	0.6465
Synthetic AUC	0.4976
Synthetic Elbow Point	0.0802
Synthetic JS Distance	0.3480