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Report generated at 2020-05-19 05:27:51

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	145749172	173400002
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	136114215	168920220
Mapped(QC-failed)	0	0
% Mapped	93.3900	97.4200
Paired	145749172	173400002
Paired(QC-failed)	0	0
Read1	72874586	86700001
Read1(QC-failed)	0	0
Read2	72874586	86700001
Read2(QC-failed)	0	0
Properly Paired	134093951	165589734
Properly Paired(QC-failed)	0	0
% Properly Paired	92.0000	95.5000
With itself	135283028	168052672
With itself(QC-failed)	0	0
Singletons	831187	867548
Singletons(QC-failed)	0	0
% Singleton	0.5700	0.5000
Diff. Chroms	655891	1552539
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	59286794	72427157
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	514075	372440
Paired Opt. Dupes	2682	2435
% Dupes/100	0.0087	0.0051

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	59283937	72396327
Distinct Read Pairs	58769891	72024241
One Read Pair	58260660	71654541
Two Read Pairs	504471	367402
NRF = Distinct/Total	0.9913	0.9949
PBC1 = OnePair/Distinct	0.9913	0.9949
PBC2 = OnePair/TwoPair	115.4886	195.0304

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	117545438	144109434
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	117545438	144109434
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	117545438	144109434
Paired(QC-failed)	0	0
Read1	58772719	72054717
Read1(QC-failed)	0	0
Read2	58772719	72054717
Read2(QC-failed)	0	0
Properly Paired	117545438	144109434
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	117545438	144109434
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	239893
Np	0
N optimal	239893
N conservative	239893
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.	150
Corr. Est. Fragment Len.	0.2079
Phantom Peak	50
Corr. Phantom Peak	0.2233
Argmin. Corr.	1500
Min. Corr.	0.1925
NSC	1.0798
RSC	0.4997

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	0.5084

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	0.1607
AUC	0.4962
CHANCE divergence	0.1419
Elbow Point	0.0000
JS Distance	0.7745
Synthetic AUC	0.5050
Synthetic Elbow Point	0.3326
Synthetic JS Distance	0.4803