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Report generated at 2020-05-20 19:18:19

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	86890000	177519184
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55475042	172494915
Mapped(QC-failed)	0	0
% Mapped	63.8500	97.1700
Paired	86890000	177519184
Paired(QC-failed)	0	0
Read1	43445000	88759592
Read1(QC-failed)	0	0
Read2	43445000	88759592
Read2(QC-failed)	0	0
Properly Paired	54441004	168093297
Properly Paired(QC-failed)	0	0
% Properly Paired	62.6600	94.6900
With itself	54718575	170816950
With itself(QC-failed)	0	0
Singletons	756467	1677965
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.9500
Diff. Chroms	103704	1509587
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	24785984	73622728
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	146164	559519
Paired Opt. Dupes	1405	3080
% Dupes/100	0.0059	0.0076

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	24782589	73528740
Distinct Read Pairs	24636448	72972791
One Read Pair	24490963	72421080
Two Read Pairs	144840	547586
NRF = Distinct/Total	0.9941	0.9924
PBC1 = OnePair/Distinct	0.9941	0.9924
PBC2 = OnePair/TwoPair	169.0898	132.2552

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	49279640	146126418
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49279640	146126418
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	49279640	146126418
Paired(QC-failed)	0	0
Read1	24639820	73063209
Read1(QC-failed)	0	0
Read2	24639820	73063209
Read2(QC-failed)	0	0
Properly Paired	49279640	146126418
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	49279640	146126418
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	119381
Np	0
N optimal	119381
N conservative	119381
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.	125
Corr. Est. Fragment Len.	0.1896
Phantom Peak	50
Corr. Phantom Peak	0.2198
Argmin. Corr.	1500
Min. Corr.	0.1690
NSC	1.1215
RSC	0.4046

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	0.2262

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	0.1841
AUC	0.4942
CHANCE divergence	0.2169
Elbow Point	0.0000
JS Distance	0.6756
Synthetic AUC	0.4989
Synthetic Elbow Point	0.1766
Synthetic JS Distance	0.3990