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Report generated at 2020-05-03 19:28:54

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	119046204	155229270
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	114243163	150942742
Mapped(QC-failed)	0	0
% Mapped	95.9700	97.2400
Paired	119046204	155229270
Paired(QC-failed)	0	0
Read1	59523102	77614635
Read1(QC-failed)	0	0
Read2	59523102	77614635
Read2(QC-failed)	0	0
Properly Paired	112400189	148607799
Properly Paired(QC-failed)	0	0
% Properly Paired	94.4200	95.7300
With itself	113578678	150154921
With itself(QC-failed)	0	0
Singletons	664485	787821
Singletons(QC-failed)	0	0
% Singleton	0.5600	0.5100
Diff. Chroms	657853	787302
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	49318239	64734644
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	251040	274227
Paired Opt. Dupes	1377	1161
% Dupes/100	0.0051	0.0042

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	49309071	64654788
Distinct Read Pairs	49058093	64382114
One Read Pair	48808580	64111697
Two Read Pairs	248082	268335
NRF = Distinct/Total	0.9949	0.9958
PBC1 = OnePair/Distinct	0.9949	0.9958
PBC2 = OnePair/TwoPair	196.7437	238.9241

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	98134398	128920834
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	98134398	128920834
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	98134398	128920834
Paired(QC-failed)	0	0
Read1	49067199	64460417
Read1(QC-failed)	0	0
Read2	49067199	64460417
Read2(QC-failed)	0	0
Properly Paired	98134398	128920834
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	98134398	128920834
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	199099
Np	0
N optimal	199099
N conservative	199099
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.	140
Corr. Est. Fragment Len.	0.1888
Phantom Peak	50
Corr. Phantom Peak	0.2052
Argmin. Corr.	1500
Min. Corr.	0.1803
NSC	1.0473
RSC	0.3421

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	0.2837

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	0.2368
AUC	0.4959
CHANCE divergence	0.1066
Elbow Point	0.0000
JS Distance	0.6823
Synthetic AUC	0.5072
Synthetic Elbow Point	0.2030
Synthetic JS Distance	0.3531