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Report generated at 2020-07-07 22:08:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	147436474	145880064
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	145509257	143543482
Mapped(QC-failed)	0	0
% Mapped	98.6900	98.4000
Paired	147436474	145880064
Paired(QC-failed)	0	0
Read1	73718237	72940032
Read1(QC-failed)	0	0
Read2	73718237	72940032
Read2(QC-failed)	0	0
Properly Paired	139152173	137661111
Properly Paired(QC-failed)	0	0
% Properly Paired	94.3800	94.3700
With itself	144492601	142561673
With itself(QC-failed)	0	0
Singletons	1016656	981809
Singletons(QC-failed)	0	0
% Singleton	0.6900	0.6700
Diff. Chroms	113876	166819
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	63823233	60849654
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	2140200	702489
Paired Opt. Dupes	2760	2259
% Dupes/100	0.0335	0.0115

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	63810988	60832324
Distinct Read Pairs	61671847	60131363
One Read Pair	59619788	59468892
Two Read Pairs	1975862	649169
NRF = Distinct/Total	0.9665	0.9885
PBC1 = OnePair/Distinct	0.9667	0.9890
PBC2 = OnePair/TwoPair	30.1741	91.6077

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	123366066	120294330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	123366066	120294330
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	123366066	120294330
Paired(QC-failed)	0	0
Read1	61683033	60147165
Read1(QC-failed)	0	0
Read2	61683033	60147165
Read2(QC-failed)	0	0
Properly Paired	123366066	120294330
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	123366066	120294330
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	187086
Np	0
N optimal	187086
N conservative	187086
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.	0.1852
Phantom Peak	45
Corr. Phantom Peak	0.1805
Argmin. Corr.	1500
Min. Corr.	0.1744
NSC	1.0620
RSC	1.7790

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	0.4274

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	0.2085
AUC	0.4963
CHANCE divergence	0.1013
Elbow Point	0.0000
JS Distance	0.7582
Synthetic AUC	0.4974
Synthetic Elbow Point	0.2905
Synthetic JS Distance	0.4064