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Report generated at 2020-07-10 11:38:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	94912066	112771886
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	93555445	109873578
Mapped(QC-failed)	0	0
% Mapped	98.5700	97.4300
Paired	94912066	112771886
Paired(QC-failed)	0	0
Read1	47456033	56385943
Read1(QC-failed)	0	0
Read2	47456033	56385943
Read2(QC-failed)	0	0
Properly Paired	81985356	84952591
Properly Paired(QC-failed)	0	0
% Properly Paired	86.3800	75.3300
With itself	92879434	108164942
With itself(QC-failed)	0	0
Singletons	676011	1708636
Singletons(QC-failed)	0	0
% Singleton	0.7100	1.5200
Diff. Chroms	9385748	19230639
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	37049670	37110419
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2777154	616930
Paired Opt. Dupes	2230	2436
% Dupes/100	0.0750	0.0166

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36895813	37079658
Distinct Read Pairs	34157994	36465928
One Read Pair	31712079	35868516
Two Read Pairs	2231225	585863
NRF = Distinct/Total	0.9258	0.9834
PBC1 = OnePair/Distinct	0.9284	0.9836
PBC2 = OnePair/TwoPair	14.2129	61.2234

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	68545032	72986978
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	68545032	72986978
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	68545032	72986978
Paired(QC-failed)	0	0
Read1	34272516	36493489
Read1(QC-failed)	0	0
Read2	34272516	36493489
Read2(QC-failed)	0	0
Properly Paired	68545032	72986978
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	68545032	72986978
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	69923
Np	0
N optimal	69923
N conservative	69923
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.	150
Corr. Est. Fragment Len.	0.2133
Phantom Peak	55
Corr. Phantom Peak	0.1813
Argmin. Corr.	1500
Min. Corr.	0.1571
NSC	1.3577
RSC	2.3193

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	0.3028

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	0.2210
AUC	0.4951
CHANCE divergence	0.1177
Elbow Point	0.0000
JS Distance	0.7286
Synthetic AUC	0.5059
Synthetic Elbow Point	0.2904
Synthetic JS Distance	0.4043