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Report generated at 2020-07-15 02:16:09

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	63671314	153209202
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61471331	149479079
Mapped(QC-failed)	0	0
% Mapped	96.5400	97.5700
Paired	63671314	153209202
Paired(QC-failed)	0	0
Read1	31835657	76604601
Read1(QC-failed)	0	0
Read2	31835657	76604601
Read2(QC-failed)	0	0
Properly Paired	60782964	147025154
Properly Paired(QC-failed)	0	0
% Properly Paired	95.4600	95.9600
With itself	61258170	148752334
With itself(QC-failed)	0	0
Singletons	213161	726745
Singletons(QC-failed)	0	0
% Singleton	0.3300	0.4700
Diff. Chroms	308768	985904
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	27958035	64022479
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	99701	238123
Paired Opt. Dupes	708	1074
% Dupes/100	0.0036	0.0037

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	27954603	63951647
Distinct Read Pairs	27854923	63714783
One Read Pair	27755538	63480345
Two Read Pairs	99091	232360
NRF = Distinct/Total	0.9964	0.9963
PBC1 = OnePair/Distinct	0.9964	0.9963
PBC2 = OnePair/TwoPair	280.1015	273.1982

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	55716668	127568712
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	55716668	127568712
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	55716668	127568712
Paired(QC-failed)	0	0
Read1	27858334	63784356
Read1(QC-failed)	0	0
Read2	27858334	63784356
Read2(QC-failed)	0	0
Properly Paired	55716668	127568712
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	55716668	127568712
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	133114
Np	0
N optimal	133114
N conservative	133114
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.	165
Corr. Est. Fragment Len.	0.1915
Phantom Peak	50
Corr. Phantom Peak	0.1931
Argmin. Corr.	1500
Min. Corr.	0.1796
NSC	1.0662
RSC	0.8833

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	0.2820

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	0.2020
AUC	0.4946
CHANCE divergence	0.1520
Elbow Point	0.0000
JS Distance	0.6889
Synthetic AUC	0.5040
Synthetic Elbow Point	0.2495
Synthetic JS Distance	0.3938