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Report generated at 2019-10-13 10:18:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	95220012	106180416
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	90865737	98634603
Mapped(QC-failed)	0	0
% Mapped	95.4300	92.8900
Paired	95220012	106180416
Paired(QC-failed)	0	0
Read1	47610006	53090208
Read1(QC-failed)	0	0
Read2	47610006	53090208
Read2(QC-failed)	0	0
Properly Paired	86970006	91384537
Properly Paired(QC-failed)	0	0
% Properly Paired	91.3400	86.0700
With itself	87564253	92607301
With itself(QC-failed)	0	0
Singletons	3301484	6027302
Singletons(QC-failed)	0	0
% Singleton	3.4700	5.6800
Diff. Chroms	332883	792771
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	36794071	37373521
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	715737	355831
Paired Opt. Dupes	4411	3074
% Dupes/100	0.0195	0.0095

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	36793001	37338415
Distinct Read Pairs	36077283	36983246
One Read Pair	35377988	36645916
Two Read Pairs	685131	328129
NRF = Distinct/Total	0.9805	0.9905
PBC1 = OnePair/Distinct	0.9806	0.9909
PBC2 = OnePair/TwoPair	51.6368	111.6814

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	72156668	74035380
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	72156668	74035380
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	72156668	74035380
Paired(QC-failed)	0	0
Read1	36078334	37017690
Read1(QC-failed)	0	0
Read2	36078334	37017690
Read2(QC-failed)	0	0
Properly Paired	72156668	74035380
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	72156668	74035380
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	142044
Np	0
N optimal	142044
N conservative	142044
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.	0.1759
Phantom Peak	50
Corr. Phantom Peak	0.1839
Argmin. Corr.	1500
Min. Corr.	0.1731
NSC	1.0167
RSC	0.2673

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	0.1660

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	0.2706
AUC	0.4952
CHANCE divergence	0.1054
Elbow Point	0.0000
JS Distance	0.6310
Synthetic AUC	0.5039
Synthetic Elbow Point	0.1290
Synthetic JS Distance	0.2927