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Report generated at 2021-02-05 16:57:04

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	52016636	128405074
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	49733754	126457897
Mapped(QC-failed)	0	0
% Mapped	95.6100	98.4800
Paired	52016636	128405074
Paired(QC-failed)	0	0
Read1	26008318	64202537
Read1(QC-failed)	0	0
Read2	26008318	64202537
Read2(QC-failed)	0	0
Properly Paired	49305252	122387045
Properly Paired(QC-failed)	0	0
% Properly Paired	94.7900	95.3100
With itself	49507867	125508177
With itself(QC-failed)	0	0
Singletons	225887	949720
Singletons(QC-failed)	0	0
% Singleton	0.4300	0.7400
Diff. Chroms	15874	158656
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	22838639	53542620
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	3043446	280947
Paired Opt. Dupes	972	2697
% Dupes/100	0.1333	0.0052

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	22807902	53433746
Distinct Read Pairs	19769180	53172146
One Read Pair	17157969	52921658
Two Read Pairs	2283976	245876
NRF = Distinct/Total	0.8668	0.9951
PBC1 = OnePair/Distinct	0.8679	0.9953
PBC2 = OnePair/TwoPair	7.5123	215.2372

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	39590386	106523346
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	39590386	106523346
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	39590386	106523346
Paired(QC-failed)	0	0
Read1	19795193	53261673
Read1(QC-failed)	0	0
Read2	19795193	53261673
Read2(QC-failed)	0	0
Properly Paired	39590386	106523346
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	39590386	106523346
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	81399
Np	0
N optimal	81399
N conservative	81399
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.	0.2832
Phantom Peak	55
Corr. Phantom Peak	0.2047
Argmin. Corr.	1500
Min. Corr.	0.1435
NSC	1.9740
RSC	2.2836

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	0.4772

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	0.1359
AUC	0.4933
CHANCE divergence	0.2280
Elbow Point	0.0000
JS Distance	0.8146
Synthetic AUC	0.5108
Synthetic Elbow Point	0.4297
Synthetic JS Distance	0.5175