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Report generated at 2020-07-10 12:42:25

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	106389950	110135000
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	104952311	107233350
Mapped(QC-failed)	0	0
% Mapped	98.6500	97.3700
Paired	106389950	110135000
Paired(QC-failed)	0	0
Read1	53194975	55067500
Read1(QC-failed)	0	0
Read2	53194975	55067500
Read2(QC-failed)	0	0
Properly Paired	87020396	85255224
Properly Paired(QC-failed)	0	0
% Properly Paired	81.7900	77.4100
With itself	103975022	105602140
With itself(QC-failed)	0	0
Singletons	977289	1631210
Singletons(QC-failed)	0	0
% Singleton	0.9200	1.4800
Diff. Chroms	14803448	16704113
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	39687781	37187240
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	657633	530724
Paired Opt. Dupes	2661	2167
% Dupes/100	0.0166	0.0143

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	39643629	37166182
Distinct Read Pairs	38992000	36637046
One Read Pair	38353489	36123457
Two Read Pairs	626864	503773
NRF = Distinct/Total	0.9836	0.9858
PBC1 = OnePair/Distinct	0.9836	0.9860
PBC2 = OnePair/TwoPair	61.1831	71.7058

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	78060296	73313032
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	78060296	73313032
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	78060296	73313032
Paired(QC-failed)	0	0
Read1	39030148	36656516
Read1(QC-failed)	0	0
Read2	39030148	36656516
Read2(QC-failed)	0	0
Properly Paired	78060296	73313032
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	78060296	73313032
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	182648
Np	0
N optimal	182648
N conservative	182648
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.	125
Corr. Est. Fragment Len.	0.1725
Phantom Peak	50
Corr. Phantom Peak	0.1731
Argmin. Corr.	1500
Min. Corr.	0.1694
NSC	1.0179
RSC	0.8215

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	0.1466

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	0.4954
CHANCE divergence	0.1105
Elbow Point	0.0000
JS Distance	0.6360
Synthetic AUC	0.5035
Synthetic Elbow Point	0.1153
Synthetic JS Distance	0.3024