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Report generated at 2019-10-13 09:52:07

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	139909130	67430072
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	133619285	65774336
Mapped(QC-failed)	0	0
% Mapped	95.5000	97.5400
Paired	139909130	67430072
Paired(QC-failed)	0	0
Read1	69954565	33715036
Read1(QC-failed)	0	0
Read2	69954565	33715036
Read2(QC-failed)	0	0
Properly Paired	131776201	65242108
Properly Paired(QC-failed)	0	0
% Properly Paired	94.1900	96.7600
With itself	132483430	65481547
With itself(QC-failed)	0	0
Singletons	1135855	292789
Singletons(QC-failed)	0	0
% Singleton	0.8100	0.4300
Diff. Chroms	120517	63993
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	53869386	28780738
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	10368993	1886510
Paired Opt. Dupes	3357	2357
% Dupes/100	0.1925	0.0655

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	53868195	28752606
Distinct Read Pairs	43499411	26868268
One Read Pair	35043519	25090950
Two Read Pairs	6884650	1676042
NRF = Distinct/Total	0.8075	0.9345
PBC1 = OnePair/Distinct	0.8056	0.9339
PBC2 = OnePair/TwoPair	5.0901	14.9704

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	87000786	53788456
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	87000786	53788456
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	87000786	53788456
Paired(QC-failed)	0	0
Read1	43500393	26894228
Read1(QC-failed)	0	0
Read2	43500393	26894228
Read2(QC-failed)	0	0
Properly Paired	87000786	53788456
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	87000786	53788456
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	71036
Np	0
N optimal	71036
N conservative	71036
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.	145
Corr. Est. Fragment Len.	0.1787
Phantom Peak	50
Corr. Phantom Peak	0.2117
Argmin. Corr.	1500
Min. Corr.	0.1684
NSC	1.0611
RSC	0.2377

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	0.0367

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	0.2881
AUC	0.4956
CHANCE divergence	0.1155
Elbow Point	0.0000
JS Distance	0.5457
Synthetic AUC	0.5031
Synthetic Elbow Point	0.0599
Synthetic JS Distance	0.2637