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Report generated at 2019-10-13 00:42:13

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	73932674	81954026
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	70866363	79524456
Mapped(QC-failed)	0	0
% Mapped	95.8500	97.0400
Paired	73932674	81954026
Paired(QC-failed)	0	0
Read1	36966337	40977013
Read1(QC-failed)	0	0
Read2	36966337	40977013
Read2(QC-failed)	0	0
Properly Paired	69751141	77093830
Properly Paired(QC-failed)	0	0
% Properly Paired	94.3400	94.0700
With itself	70521486	79098584
With itself(QC-failed)	0	0
Singletons	344877	425872
Singletons(QC-failed)	0	0
% Singleton	0.4700	0.5200
Diff. Chroms	398840	1402744
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	30822545	34184517
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	475838	147561
Paired Opt. Dupes	7745	4430
% Dupes/100	0.0154	0.0043

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	30821739	34160894
Distinct Read Pairs	30345912	34013583
One Read Pair	29875983	33872187
Two Read Pairs	464175	138075
NRF = Distinct/Total	0.9846	0.9957
PBC1 = OnePair/Distinct	0.9845	0.9958
PBC2 = OnePair/TwoPair	64.3636	245.3173

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	60693414	68073912
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	60693414	68073912
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	60693414	68073912
Paired(QC-failed)	0	0
Read1	30346707	34036956
Read1(QC-failed)	0	0
Read2	30346707	34036956
Read2(QC-failed)	0	0
Properly Paired	60693414	68073912
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	60693414	68073912
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	48505
Np	0
N optimal	48505
N conservative	48505
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.	0.1892
Phantom Peak	50
Corr. Phantom Peak	0.1996
Argmin. Corr.	1500
Min. Corr.	0.1731
NSC	1.0930
RSC	0.6074

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	0.1357

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	0.2863
AUC	0.4948
CHANCE divergence	0.1070
Elbow Point	0.0000
JS Distance	0.5962
Synthetic AUC	0.4957
Synthetic Elbow Point	0.1646
Synthetic JS Distance	0.2843