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Report generated at 2020-05-18 11:13:23

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52348320	173400002
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	50633920	168920220
Mapped(QC-failed)	0	0
% Mapped	96.7300	97.4200
Paired	52348320	173400002
Paired(QC-failed)	0	0
Read1	26174160	86700001
Read1(QC-failed)	0	0
Read2	26174160	86700001
Read2(QC-failed)	0	0
Properly Paired	49975387	165589734
Properly Paired(QC-failed)	0	0
% Properly Paired	95.4700	95.5000
With itself	50453014	168052672
With itself(QC-failed)	0	0
Singletons	180906	867548
Singletons(QC-failed)	0	0
% Singleton	0.3500	0.5000
Diff. Chroms	324379	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	22896461	72427157
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	82630	372440
Paired Opt. Dupes	996	2435
% Dupes/100	0.0036	0.0051

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22895676	72396327
Distinct Read Pairs	22813048	72024241
One Read Pair	22730645	71654541
Two Read Pairs	82178	367402
NRF = Distinct/Total	0.9964	0.9949
PBC1 = OnePair/Distinct	0.9964	0.9949
PBC2 = OnePair/TwoPair	276.6026	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	45627662	144109434
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	45627662	144109434
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	45627662	144109434
Paired(QC-failed)	0	0
Read1	22813831	72054717
Read1(QC-failed)	0	0
Read2	22813831	72054717
Read2(QC-failed)	0	0
Properly Paired	45627662	144109434
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	45627662	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	105033
Np	0
N optimal	105033
N conservative	105033
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.	0.1893
Phantom Peak	50
Corr. Phantom Peak	0.1922
Argmin. Corr.	1500
Min. Corr.	0.1786
NSC	1.0605
RSC	0.7930

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	0.2365

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	0.2071
AUC	0.4940
CHANCE divergence	0.1649
Elbow Point	0.0000
JS Distance	0.6736
Synthetic AUC	0.4971
Synthetic Elbow Point	0.2208
Synthetic JS Distance	0.3768