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Report generated at 2021-02-05 18:59:46

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	107714400	128405074
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	106404361	126457897
Mapped(QC-failed)	0	0
% Mapped	98.7800	98.4800
Paired	107714400	128405074
Paired(QC-failed)	0	0
Read1	53857200	64202537
Read1(QC-failed)	0	0
Read2	53857200	64202537
Read2(QC-failed)	0	0
Properly Paired	104591969	122387045
Properly Paired(QC-failed)	0	0
% Properly Paired	97.1000	95.3100
With itself	105703548	125508177
With itself(QC-failed)	0	0
Singletons	700813	949720
Singletons(QC-failed)	0	0
% Singleton	0.6500	0.7400
Diff. Chroms	72008	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	46005320	53542620
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	484439	280947
Paired Opt. Dupes	2113	2697
% Dupes/100	0.0105	0.0052

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	45867184	53433746
Distinct Read Pairs	45406152	53172146
One Read Pair	44951071	52921658
Two Read Pairs	450028	245876
NRF = Distinct/Total	0.9899	0.9951
PBC1 = OnePair/Distinct	0.9900	0.9953
PBC2 = OnePair/TwoPair	99.8851	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	91041762	106523346
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	91041762	106523346
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	91041762	106523346
Paired(QC-failed)	0	0
Read1	45520881	53261673
Read1(QC-failed)	0	0
Read2	45520881	53261673
Read2(QC-failed)	0	0
Properly Paired	91041762	106523346
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	91041762	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	95539
Np	0
N optimal	95539
N conservative	95539
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.	0.1779
Phantom Peak	50
Corr. Phantom Peak	0.1810
Argmin. Corr.	1500
Min. Corr.	0.1730
NSC	1.0282
RSC	0.6120

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	0.0638

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	0.2926
AUC	0.4956
CHANCE divergence	0.1036
Elbow Point	0.0000
JS Distance	0.5747
Synthetic AUC	0.5078
Synthetic Elbow Point	0.0884
Synthetic JS Distance	0.2567