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Report generated at 2020-07-10 18:05:15

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	193988394	136244046
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	191034452	134324819
Mapped(QC-failed)	0	0
% Mapped	98.4800	98.5900
Paired	193988394	136244046
Paired(QC-failed)	0	0
Read1	96994197	68122023
Read1(QC-failed)	0	0
Read2	96994197	68122023
Read2(QC-failed)	0	0
Properly Paired	189158408	131038518
Properly Paired(QC-failed)	0	0
% Properly Paired	97.5100	96.1800
With itself	190106293	133591989
With itself(QC-failed)	0	0
Singletons	928159	732830
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5400
Diff. Chroms	107540	172253
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	83098993	57476635
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1548734	368798
Paired Opt. Dupes	4004	2996
% Dupes/100	0.0186	0.0064

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	83020709	57449552
Distinct Read Pairs	81483318	57083273
One Read Pair	79979446	56730634
Two Read Pairs	1475521	346986
NRF = Distinct/Total	0.9815	0.9936
PBC1 = OnePair/Distinct	0.9815	0.9938
PBC2 = OnePair/TwoPair	54.2042	163.4955

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	163100518	114215674
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	163100518	114215674
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	163100518	114215674
Paired(QC-failed)	0	0
Read1	81550259	57107837
Read1(QC-failed)	0	0
Read2	81550259	57107837
Read2(QC-failed)	0	0
Properly Paired	163100518	114215674
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	163100518	114215674
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	88128
Np	0
N optimal	88128
N conservative	88128
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.	115
Corr. Est. Fragment Len.	0.1725
Phantom Peak	50
Corr. Phantom Peak	0.1789
Argmin. Corr.	1500
Min. Corr.	0.1686
NSC	1.0235
RSC	0.3829

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	0.0428

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	0.3437
AUC	0.4968
CHANCE divergence	0.0951
Elbow Point	0.0000
JS Distance	0.5125
Synthetic AUC	0.5050
Synthetic Elbow Point	0.0392
Synthetic JS Distance	0.1837