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Report generated at 2019-11-03 16:29:01

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	90112742	194166736
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	88102989	188427054
Mapped(QC-failed)	0	0
% Mapped	97.7700	97.0400
Paired	90112742	194166736
Paired(QC-failed)	0	0
Read1	45056371	97083368
Read1(QC-failed)	0	0
Read2	45056371	97083368
Read2(QC-failed)	0	0
Properly Paired	86591121	183258385
Properly Paired(QC-failed)	0	0
% Properly Paired	96.0900	94.3800
With itself	87548476	186937146
With itself(QC-failed)	0	0
Singletons	554513	1489908
Singletons(QC-failed)	0	0
% Singleton	0.6200	0.7700
Diff. Chroms	131721	1235264
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	39848362	80987770
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2032095	1179794
Paired Opt. Dupes	5119	10644
% Dupes/100	0.0510	0.0146

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39841965	80909491
Distinct Read Pairs	37810194	79732095
One Read Pair	35862238	78571982
Two Read Pairs	1867547	1145607
NRF = Distinct/Total	0.9490	0.9854
PBC1 = OnePair/Distinct	0.9485	0.9855
PBC2 = OnePair/TwoPair	19.2029	68.5855

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	75632534	159615952
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75632534	159615952
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75632534	159615952
Paired(QC-failed)	0	0
Read1	37816267	79807976
Read1(QC-failed)	0	0
Read2	37816267	79807976
Read2(QC-failed)	0	0
Properly Paired	75632534	159615952
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75632534	159615952
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	113015
Np	0
N optimal	113015
N conservative	113015
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.	155
Corr. Est. Fragment Len.	0.1954
Phantom Peak	50
Corr. Phantom Peak	0.1969
Argmin. Corr.	1500
Min. Corr.	0.1787
NSC	1.0932
RSC	0.9169

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	0.3759

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	0.2017
AUC	0.4953
CHANCE divergence	0.1172
Elbow Point	0.0000
JS Distance	0.7507
Synthetic AUC	0.4989
Synthetic Elbow Point	0.3276
Synthetic JS Distance	0.4203