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Report generated at 2021-02-06 08:36:56

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	109221030	128405074
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	108133922	126457897
Mapped(QC-failed)	0	0
% Mapped	99.0000	98.4800
Paired	109221030	128405074
Paired(QC-failed)	0	0
Read1	54610515	64202537
Read1(QC-failed)	0	0
Read2	54610515	64202537
Read2(QC-failed)	0	0
Properly Paired	106899899	122387045
Properly Paired(QC-failed)	0	0
% Properly Paired	97.8700	95.3100
With itself	107441819	125508177
With itself(QC-failed)	0	0
Singletons	692103	949720
Singletons(QC-failed)	0	0
% Singleton	0.6300	0.7400
Diff. Chroms	55049	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	48986277	53542620
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	376556	280947
Paired Opt. Dupes	1276	2697
% Dupes/100	0.0077	0.0052

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	48890693	53433746
Distinct Read Pairs	48526118	53172146
One Read Pair	48165171	52921658
Two Read Pairs	357498	245876
NRF = Distinct/Total	0.9925	0.9951
PBC1 = OnePair/Distinct	0.9926	0.9953
PBC2 = OnePair/TwoPair	134.7285	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	97219442	106523346
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	97219442	106523346
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	97219442	106523346
Paired(QC-failed)	0	0
Read1	48609721	53261673
Read1(QC-failed)	0	0
Read2	48609721	53261673
Read2(QC-failed)	0	0
Properly Paired	97219442	106523346
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	97219442	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	208884
Np	0
N optimal	208884
N conservative	208884
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.	0.1807
Phantom Peak	45
Corr. Phantom Peak	0.1789
Argmin. Corr.	1500
Min. Corr.	0.1699
NSC	1.0639
RSC	1.2047

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	0.3348

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	0.2349
AUC	0.4957
CHANCE divergence	0.1084
Elbow Point	0.0000
JS Distance	0.7118
Synthetic AUC	0.4961
Synthetic Elbow Point	0.2182
Synthetic JS Distance	0.3555