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Report generated at 2019-11-03 15:11:34

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	143736964	213968900
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	142202268	211195024
Mapped(QC-failed)	0	0
% Mapped	98.9300	98.7000
Paired	143736964	213968900
Paired(QC-failed)	0	0
Read1	71868482	106984450
Read1(QC-failed)	0	0
Read2	71868482	106984450
Read2(QC-failed)	0	0
Properly Paired	140521496	206798914
Properly Paired(QC-failed)	0	0
% Properly Paired	97.7600	96.6500
With itself	141512669	210073494
With itself(QC-failed)	0	0
Singletons	689599	1121530
Singletons(QC-failed)	0	0
% Singleton	0.4800	0.5200
Diff. Chroms	608102	2031909
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	64566060	91477404
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8236717	2315030
Paired Opt. Dupes	19226	43440
% Dupes/100	0.1276	0.0253

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	64564882	91372844
Distinct Read Pairs	56328298	89062444
One Read Pair	48962351	86800060
Two Read Pairs	6575657	2218941
NRF = Distinct/Total	0.8724	0.9747
PBC1 = OnePair/Distinct	0.8692	0.9746
PBC2 = OnePair/TwoPair	7.4460	39.1178

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	112658686	178324748
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	112658686	178324748
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	112658686	178324748
Paired(QC-failed)	0	0
Read1	56329343	89162374
Read1(QC-failed)	0	0
Read2	56329343	89162374
Read2(QC-failed)	0	0
Properly Paired	112658686	178324748
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	112658686	178324748
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	44152
Np	0
N optimal	44152
N conservative	44152
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.	205
Corr. Est. Fragment Len.	0.4511
Phantom Peak	55
Corr. Phantom Peak	0.4190
Argmin. Corr.	1500
Min. Corr.	0.1844
NSC	2.4462
RSC	1.1372

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	0.6535

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	0.1111
AUC	0.4962
CHANCE divergence	0.1175
Elbow Point	0.0000
JS Distance	0.9496
Synthetic AUC	0.4977
Synthetic Elbow Point	0.6006
Synthetic JS Distance	0.6406