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Report generated at 2019-11-03 16:38:53

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	156057922	151544194
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	154809579	148910512
Mapped(QC-failed)	0	0
% Mapped	99.2000	98.2600
Paired	156057922	151544194
Paired(QC-failed)	0	0
Read1	78028961	75772097
Read1(QC-failed)	0	0
Read2	78028961	75772097
Read2(QC-failed)	0	0
Properly Paired	153159173	146074541
Properly Paired(QC-failed)	0	0
% Properly Paired	98.1400	96.3900
With itself	154196357	147974444
With itself(QC-failed)	0	0
Singletons	613222	936068
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.6200
Diff. Chroms	336218	884346
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	70153157	64801692
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	1280612	1185579
Paired Opt. Dupes	15281	14661
% Dupes/100	0.0183	0.0183

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	70152115	64733526
Distinct Read Pairs	68871527	63550092
One Read Pair	67610127	62385083
Two Read Pairs	1242489	1147263
NRF = Distinct/Total	0.9817	0.9817
PBC1 = OnePair/Distinct	0.9817	0.9817
PBC2 = OnePair/TwoPair	54.4151	54.3773

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	137745090	127232226
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	137745090	127232226
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	137745090	127232226
Paired(QC-failed)	0	0
Read1	68872545	63616113
Read1(QC-failed)	0	0
Read2	68872545	63616113
Read2(QC-failed)	0	0
Properly Paired	137745090	127232226
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	137745090	127232226
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	220595
Np	0
N optimal	220595
N conservative	220595
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.	0.1836
Phantom Peak	50
Corr. Phantom Peak	0.1847
Argmin. Corr.	1500
Min. Corr.	0.1818
NSC	1.0100
RSC	0.6378

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	0.4877

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	0.1816
AUC	0.4965
CHANCE divergence	0.1176
Elbow Point	0.0000
JS Distance	0.7079
Synthetic AUC	0.5008
Synthetic Elbow Point	0.3336
Synthetic JS Distance	0.4470