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Report generated at 2020-05-14 13:13:31

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65683494	91936088
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61454021	86108967
Mapped(QC-failed)	0	0
% Mapped	93.5600	93.6600
Paired	65683494	91936088
Paired(QC-failed)	0	0
Read1	32841747	45968044
Read1(QC-failed)	0	0
Read2	32841747	45968044
Read2(QC-failed)	0	0
Properly Paired	60495400	74610692
Properly Paired(QC-failed)	0	0
% Properly Paired	92.1000	81.1500
With itself	60997700	83414092
With itself(QC-failed)	0	0
Singletons	456321	2694875
Singletons(QC-failed)	0	0
% Singleton	0.6900	2.9300
Diff. Chroms	263097	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	26500960	28516779
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	154895	321586
Paired Opt. Dupes	775	641
% Dupes/100	0.0058	0.0113

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26493515	28515658
Distinct Read Pairs	26338672	28194090
One Read Pair	26184597	27875944
Two Read Pairs	153310	314754
NRF = Distinct/Total	0.9942	0.9887
PBC1 = OnePair/Distinct	0.9941	0.9887
PBC2 = OnePair/TwoPair	170.7951	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	52692130	56390386
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52692130	56390386
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52692130	56390386
Paired(QC-failed)	0	0
Read1	26346065	28195193
Read1(QC-failed)	0	0
Read2	26346065	28195193
Read2(QC-failed)	0	0
Properly Paired	52692130	56390386
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52692130	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	128352
Np	0
N optimal	128352
N conservative	128352
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.	145
Corr. Est. Fragment Len.	0.1985
Phantom Peak	50
Corr. Phantom Peak	0.2069
Argmin. Corr.	1500
Min. Corr.	0.1874
NSC	1.0596
RSC	0.5705

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	0.1876

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	0.1808
AUC	0.4944
CHANCE divergence	0.2009
Elbow Point	0.0000
JS Distance	0.6956
Synthetic AUC	0.5052
Synthetic Elbow Point	0.1436
Synthetic JS Distance	0.4109