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Report generated at 2020-07-15 01:44:41

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	184040704	145880064
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	181068194	143543482
Mapped(QC-failed)	0	0
% Mapped	98.3800	98.4000
Paired	184040704	145880064
Paired(QC-failed)	0	0
Read1	92020352	72940032
Read1(QC-failed)	0	0
Read2	92020352	72940032
Read2(QC-failed)	0	0
Properly Paired	179054344	137661111
Properly Paired(QC-failed)	0	0
% Properly Paired	97.2900	94.3700
With itself	180358923	142561673
With itself(QC-failed)	0	0
Singletons	709271	981809
Singletons(QC-failed)	0	0
% Singleton	0.3900	0.6700
Diff. Chroms	53479	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	84027680	60849654
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	53243195	702489
Paired Opt. Dupes	11998	2259
% Dupes/100	0.6336	0.0115

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	84002755	60832324
Distinct Read Pairs	30775906	60131363
One Read Pair	8942111	59468892
Two Read Pairs	7885608	649169
NRF = Distinct/Total	0.3664	0.9885
PBC1 = OnePair/Distinct	0.2906	0.9890
PBC2 = OnePair/TwoPair	1.1340	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	61568970	120294330
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	61568970	120294330
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	61568970	120294330
Paired(QC-failed)	0	0
Read1	30784485	60147165
Read1(QC-failed)	0	0
Read2	30784485	60147165
Read2(QC-failed)	0	0
Properly Paired	61568970	120294330
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	61568970	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	60025
Np	0
N optimal	60025
N conservative	60025
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.	145
Corr. Est. Fragment Len.	0.3221
Phantom Peak	55
Corr. Phantom Peak	0.2195
Argmin. Corr.	1500
Min. Corr.	0.1776
NSC	1.8134
RSC	3.4455

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	0.6612

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	0.0811
AUC	0.4948
CHANCE divergence	0.2491
Elbow Point	0.0000
JS Distance	0.8981
Synthetic AUC	0.5093
Synthetic Elbow Point	0.5836
Synthetic JS Distance	0.6469