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Report generated at 2019-10-13 09:17:08

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	105106116	117734680
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	102455985	114419474
Mapped(QC-failed)	0	0
% Mapped	97.4800	97.1800
Paired	105106116	117734680
Paired(QC-failed)	0	0
Read1	52553058	58867340
Read1(QC-failed)	0	0
Read2	52553058	58867340
Read2(QC-failed)	0	0
Properly Paired	101082104	106794606
Properly Paired(QC-failed)	0	0
% Properly Paired	96.1700	90.7100
With itself	101555847	112779340
With itself(QC-failed)	0	0
Singletons	900138	1640134
Singletons(QC-failed)	0	0
% Singleton	0.8600	1.3900
Diff. Chroms	179970	4519360
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	44306760	44871469
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	6651737	32327508
Paired Opt. Dupes	3058	5828
% Dupes/100	0.1501	0.7204

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	44306322	44834362
Distinct Read Pairs	37654646	12531592
One Read Pair	31923299	4645701
Two Read Pairs	4933654	1813827
NRF = Distinct/Total	0.8499	0.2795
PBC1 = OnePair/Distinct	0.8478	0.3707
PBC2 = OnePair/TwoPair	6.4705	2.5613

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	75310046	25087922
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	75310046	25087922
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	75310046	25087922
Paired(QC-failed)	0	0
Read1	37655023	12543961
Read1(QC-failed)	0	0
Read2	37655023	12543961
Read2(QC-failed)	0	0
Properly Paired	75310046	25087922
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	75310046	25087922
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	54639
Np	0
N optimal	54639
N conservative	54639
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.	0.1725
Phantom Peak	50
Corr. Phantom Peak	0.1777
Argmin. Corr.	1500
Min. Corr.	0.1671
NSC	1.0322
RSC	0.5089

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	0.1032

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	0.2543
AUC	0.4953
CHANCE divergence	0.1214
Elbow Point	0.0000
JS Distance	0.6171
Synthetic AUC	0.4998
Synthetic Elbow Point	0.1087
Synthetic JS Distance	0.3166