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Report generated at 2019-10-31 17:33:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	209674326	239432188
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	202269945	231429253
Mapped(QC-failed)	0	0
% Mapped	96.4700	96.6600
Paired	209674326	239432188
Paired(QC-failed)	0	0
Read1	104837163	119716094
Read1(QC-failed)	0	0
Read2	104837163	119716094
Read2(QC-failed)	0	0
Properly Paired	198218519	226374121
Properly Paired(QC-failed)	0	0
% Properly Paired	94.5400	94.5500
With itself	200453120	229579189
With itself(QC-failed)	0	0
Singletons	1816825	1850064
Singletons(QC-failed)	0	0
% Singleton	0.8700	0.7700
Diff. Chroms	1494951	2056124
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	82936775	93939937
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8990011	11899048
Paired Opt. Dupes	39473	28578
% Dupes/100	0.1084	0.1267

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	82936132	93919009
Distinct Read Pairs	73946191	82022723
One Read Pair	65807922	71424617
Two Read Pairs	7360530	9428354
NRF = Distinct/Total	0.8916	0.8733
PBC1 = OnePair/Distinct	0.8899	0.8708
PBC2 = OnePair/TwoPair	8.9406	7.5755

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	147893528	164081778
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	147893528	164081778
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	147893528	164081778
Paired(QC-failed)	0	0
Read1	73946764	82040889
Read1(QC-failed)	0	0
Read2	73946764	82040889
Read2(QC-failed)	0	0
Properly Paired	147893528	164081778
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	147893528	164081778
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	217205
Np	0
N optimal	217205
N conservative	217205
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.	220
Corr. Est. Fragment Len.	0.1721
Phantom Peak	50
Corr. Phantom Peak	0.1759
Argmin. Corr.	1500
Min. Corr.	0.1700
NSC	1.0127
RSC	0.3607

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	0.2139

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	0.2619
AUC	0.4959
CHANCE divergence	0.1092
Elbow Point	0.0000
JS Distance	0.5895
Synthetic AUC	0.5011
Synthetic Elbow Point	0.1801
Synthetic JS Distance	0.3111