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Report generated at 2019-11-03 23:57:10

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	204482552	155278814
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	202582649	152204810
Mapped(QC-failed)	0	0
% Mapped	99.0700	98.0200
Paired	204482552	155278814
Paired(QC-failed)	0	0
Read1	102241276	77639407
Read1(QC-failed)	0	0
Read2	102241276	77639407
Read2(QC-failed)	0	0
Properly Paired	200485020	149315055
Properly Paired(QC-failed)	0	0
% Properly Paired	98.0500	96.1600
With itself	201805353	151298295
With itself(QC-failed)	0	0
Singletons	777296	906515
Singletons(QC-failed)	0	0
% Singleton	0.3800	0.5800
Diff. Chroms	517375	1045401
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	89941040	66029859
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3734705	1524871
Paired Opt. Dupes	20929	14661
% Dupes/100	0.0415	0.0231

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	89940396	65968445
Distinct Read Pairs	86205721	64445697
One Read Pair	82595044	62945345
Two Read Pairs	3490754	1479272
NRF = Distinct/Total	0.9585	0.9769
PBC1 = OnePair/Distinct	0.9581	0.9767
PBC2 = OnePair/TwoPair	23.6611	42.5516

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	172412670	129009976
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	172412670	129009976
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	172412670	129009976
Paired(QC-failed)	0	0
Read1	86206335	64504988
Read1(QC-failed)	0	0
Read2	86206335	64504988
Read2(QC-failed)	0	0
Properly Paired	172412670	129009976
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	172412670	129009976
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	164290
Np	0
N optimal	164290
N conservative	164290
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.	195
Corr. Est. Fragment Len.	0.1721
Phantom Peak	50
Corr. Phantom Peak	0.1753
Argmin. Corr.	1500
Min. Corr.	0.1708
NSC	1.0078
RSC	0.2971

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	0.1148

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	0.3055
AUC	0.4969
CHANCE divergence	0.0939
Elbow Point	0.0000
JS Distance	0.5382
Synthetic AUC	0.5038
Synthetic Elbow Point	0.1012
Synthetic JS Distance	0.2477