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Report generated at 2019-11-03 08:48:26

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	80125580	194166736
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78497203	188427054
Mapped(QC-failed)	0	0
% Mapped	97.9700	97.0400
Paired	80125580	194166736
Paired(QC-failed)	0	0
Read1	40062790	97083368
Read1(QC-failed)	0	0
Read2	40062790	97083368
Read2(QC-failed)	0	0
Properly Paired	77371903	183258385
Properly Paired(QC-failed)	0	0
% Properly Paired	96.5600	94.3800
With itself	78014479	186937146
With itself(QC-failed)	0	0
Singletons	482724	1489908
Singletons(QC-failed)	0	0
% Singleton	0.6000	0.7700
Diff. Chroms	93731	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	35144235	80987770
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2047212	1179794
Paired Opt. Dupes	4110	10644
% Dupes/100	0.0583	0.0146

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	35136087	80909491
Distinct Read Pairs	33089373	79732095
One Read Pair	31143417	78571982
Two Read Pairs	1849827	1145607
NRF = Distinct/Total	0.9417	0.9854
PBC1 = OnePair/Distinct	0.9412	0.9855
PBC2 = OnePair/TwoPair	16.8359	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	66194046	159615952
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	66194046	159615952
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	66194046	159615952
Paired(QC-failed)	0	0
Read1	33097023	79807976
Read1(QC-failed)	0	0
Read2	33097023	79807976
Read2(QC-failed)	0	0
Properly Paired	66194046	159615952
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	66194046	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	32345
Np	0
N optimal	32345
N conservative	32345
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.	170
Corr. Est. Fragment Len.	0.3518
Phantom Peak	55
Corr. Phantom Peak	0.3339
Argmin. Corr.	1500
Min. Corr.	0.1815
NSC	1.9383
RSC	1.1174

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	0.4733

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	0.1666
AUC	0.4950
CHANCE divergence	0.1220
Elbow Point	0.0000
JS Distance	0.8687
Synthetic AUC	0.4957
Synthetic Elbow Point	0.4710
Synthetic JS Distance	0.5259