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Report generated at 2019-10-26 09:04:17

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	83634216	294654588
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	81400834	290510210
Mapped(QC-failed)	0	0
% Mapped	97.3300	98.5900
Paired	83634216	294654588
Paired(QC-failed)	0	0
Read1	41817108	147327294
Read1(QC-failed)	0	0
Read2	41817108	147327294
Read2(QC-failed)	0	0
Properly Paired	80503241	281900859
Properly Paired(QC-failed)	0	0
% Properly Paired	96.2600	95.6700
With itself	81015955	288529717
With itself(QC-failed)	0	0
Singletons	384879	1980493
Singletons(QC-failed)	0	0
% Singleton	0.4600	0.6700
Diff. Chroms	88131	3476801
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	33108654	117328478
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	29333267	14788109
Paired Opt. Dupes	7474	29230
% Dupes/100	0.8860	0.1260

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	33107088	117267661
Distinct Read Pairs	3775198	102488519
One Read Pair	499827	89380125
Two Read Pairs	352872	11628471
NRF = Distinct/Total	0.1140	0.8740
PBC1 = OnePair/Distinct	0.1324	0.8721
PBC2 = OnePair/TwoPair	1.4165	7.6863

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	7550774	205080738
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	7550774	205080738
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	7550774	205080738
Paired(QC-failed)	0	0
Read1	3775387	102540369
Read1(QC-failed)	0	0
Read2	3775387	102540369
Read2(QC-failed)	0	0
Properly Paired	7550774	205080738
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	7550774	205080738
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	24501
Np	0
N optimal	24501
N conservative	24501
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.	130
Corr. Est. Fragment Len.	0.0399
Phantom Peak	50
Corr. Phantom Peak	0.0445
Argmin. Corr.	1500
Min. Corr.	0.0373
NSC	1.0685
RSC	0.3550

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	0.0556

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	0.1612
AUC	0.4819
CHANCE divergence	0.5069
Elbow Point	0.0000
JS Distance	0.6195
Synthetic AUC	0.5009
Synthetic Elbow Point	0.1461
Synthetic JS Distance	0.2281