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Report generated at 2020-05-13 07:23:58

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	65015912	44822058
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	62233712	42270277
Mapped(QC-failed)	0	0
% Mapped	95.7200	94.3100
Paired	65015912	44822058
Paired(QC-failed)	0	0
Read1	32507956	22411029
Read1(QC-failed)	0	0
Read2	32507956	22411029
Read2(QC-failed)	0	0
Properly Paired	59467811	39106937
Properly Paired(QC-failed)	0	0
% Properly Paired	91.4700	87.2500
With itself	61254702	41498214
With itself(QC-failed)	0	0
Singletons	979010	772063
Singletons(QC-failed)	0	0
% Singleton	1.5100	1.7200
Diff. Chroms	1308770	1698756
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	26548484	17000414
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	203924	184749
Paired Opt. Dupes	2449	1571
% Dupes/100	0.0077	0.0109

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26548174	16997550
Distinct Read Pairs	26344252	16812850
One Read Pair	26141592	16629884
Two Read Pairs	201408	181248
NRF = Distinct/Total	0.9923	0.9891
PBC1 = OnePair/Distinct	0.9923	0.9891
PBC2 = OnePair/TwoPair	129.7942	91.7521

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	52689120	33631330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	52689120	33631330
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	52689120	33631330
Paired(QC-failed)	0	0
Read1	26344560	16815665
Read1(QC-failed)	0	0
Read2	26344560	16815665
Read2(QC-failed)	0	0
Properly Paired	52689120	33631330
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	52689120	33631330
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	118704
Np	0
N optimal	118704
N conservative	118704
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.	260
Corr. Est. Fragment Len.	0.2009
Phantom Peak	50
Corr. Phantom Peak	0.1941
Argmin. Corr.	1500
Min. Corr.	0.1837
NSC	1.0936
RSC	1.6660

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	0.2237

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	0.1397
AUC	0.4943
CHANCE divergence	0.3886
Elbow Point	0.0000
JS Distance	0.6871
Synthetic AUC	0.4992
Synthetic Elbow Point	0.1250
Synthetic JS Distance	0.4090