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Report generated at 2020-05-10 11:47:18

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	42474774	49040330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	33801902	43899885
Mapped(QC-failed)	0	0
% Mapped	79.5800	89.5200
Paired	42474774	49040330
Paired(QC-failed)	0	0
Read1	21237387	24520165
Read1(QC-failed)	0	0
Read2	21237387	24520165
Read2(QC-failed)	0	0
Properly Paired	26111617	30373686
Properly Paired(QC-failed)	0	0
% Properly Paired	61.4800	61.9400
With itself	32331477	41523513
With itself(QC-failed)	0	0
Singletons	1470425	2376372
Singletons(QC-failed)	0	0
% Singleton	3.4600	4.8500
Diff. Chroms	5052056	7654539
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	10370755	10159811
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	268578	264224
Paired Opt. Dupes	1473	1355
% Dupes/100	0.0259	0.0260

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	10369423	10158782
Distinct Read Pairs	10100876	9894586
One Read Pair	9838217	9636269
Two Read Pairs	256885	252589
NRF = Distinct/Total	0.9741	0.9740
PBC1 = OnePair/Distinct	0.9740	0.9739
PBC2 = OnePair/TwoPair	38.2981	38.1500

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	20204354	19791174
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	20204354	19791174
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	20204354	19791174
Paired(QC-failed)	0	0
Read1	10102177	9895587
Read1(QC-failed)	0	0
Read2	10102177	9895587
Read2(QC-failed)	0	0
Properly Paired	20204354	19791174
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	20204354	19791174
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	89015
Np	0
N optimal	89015
N conservative	89015
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.	235
Corr. Est. Fragment Len.	0.2114
Phantom Peak	50
Corr. Phantom Peak	0.2110
Argmin. Corr.	1500
Min. Corr.	0.1887
NSC	1.1207
RSC	1.0198

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	0.2878

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	0.1022
AUC	0.4909
CHANCE divergence	0.4768
Elbow Point	0.0000
JS Distance	0.7728
Synthetic AUC	0.5113
Synthetic Elbow Point	0.1346
Synthetic JS Distance	0.4517