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Report generated at 2020-05-14 18:59:40

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	131240258	91936088
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	127944327	86108967
Mapped(QC-failed)	0	0
% Mapped	97.4900	93.6600
Paired	131240258	91936088
Paired(QC-failed)	0	0
Read1	65620129	45968044
Read1(QC-failed)	0	0
Read2	65620129	45968044
Read2(QC-failed)	0	0
Properly Paired	126613634	74610692
Properly Paired(QC-failed)	0	0
% Properly Paired	96.4700	81.1500
With itself	127423804	83414092
With itself(QC-failed)	0	0
Singletons	520523	2694875
Singletons(QC-failed)	0	0
% Singleton	0.4000	2.9300
Diff. Chroms	510100	6003117
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	58690153	28516779
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	365095	321586
Paired Opt. Dupes	2220	641
% Dupes/100	0.0062	0.0113

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	58682937	28515658
Distinct Read Pairs	58317884	28194090
One Read Pair	57955028	27875944
Two Read Pairs	360677	314754
NRF = Distinct/Total	0.9938	0.9887
PBC1 = OnePair/Distinct	0.9938	0.9887
PBC2 = OnePair/TwoPair	160.6840	88.5642

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	116650116	56390386
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	116650116	56390386
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	116650116	56390386
Paired(QC-failed)	0	0
Read1	58325058	28195193
Read1(QC-failed)	0	0
Read2	58325058	28195193
Read2(QC-failed)	0	0
Properly Paired	116650116	56390386
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	116650116	56390386
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	172475
Np	0
N optimal	172475
N conservative	172475
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.	170
Corr. Est. Fragment Len.	0.2033
Phantom Peak	50
Corr. Phantom Peak	0.2005
Argmin. Corr.	1500
Min. Corr.	0.1877
NSC	1.0832
RSC	1.2162

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	0.2675

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	0.1694
AUC	0.4962
CHANCE divergence	0.1629
Elbow Point	0.0000
JS Distance	0.7211
Synthetic AUC	0.5069
Synthetic Elbow Point	0.1313
Synthetic JS Distance	0.4557