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Report generated at 2021-02-06 05:27:14

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	112771130	128405074
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	111261356	126457897
Mapped(QC-failed)	0	0
% Mapped	98.6600	98.4800
Paired	112771130	128405074
Paired(QC-failed)	0	0
Read1	56385565	64202537
Read1(QC-failed)	0	0
Read2	56385565	64202537
Read2(QC-failed)	0	0
Properly Paired	109938093	122387045
Properly Paired(QC-failed)	0	0
% Properly Paired	97.4900	95.3100
With itself	110469579	125508177
With itself(QC-failed)	0	0
Singletons	791777	949720
Singletons(QC-failed)	0	0
% Singleton	0.7000	0.7400
Diff. Chroms	64427	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	47844457	53542620
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	471886	280947
Paired Opt. Dupes	2203	2697
% Dupes/100	0.0099	0.0052

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	47638100	53433746
Distinct Read Pairs	47209618	53172146
One Read Pair	46785480	52921658
Two Read Pairs	420178	245876
NRF = Distinct/Total	0.9910	0.9951
PBC1 = OnePair/Distinct	0.9910	0.9953
PBC2 = OnePair/TwoPair	111.3468	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	94745142	106523346
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	94745142	106523346
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	94745142	106523346
Paired(QC-failed)	0	0
Read1	47372571	53261673
Read1(QC-failed)	0	0
Read2	47372571	53261673
Read2(QC-failed)	0	0
Properly Paired	94745142	106523346
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	94745142	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	48121
Np	0
N optimal	48121
N conservative	48121
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.	115
Corr. Est. Fragment Len.	0.1718
Phantom Peak	50
Corr. Phantom Peak	0.1776
Argmin. Corr.	1500
Min. Corr.	0.1682
NSC	1.0215
RSC	0.3828

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	0.0307

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	0.3306
AUC	0.4957
CHANCE divergence	0.1001
Elbow Point	0.0000
JS Distance	0.5202
Synthetic AUC	0.5002
Synthetic Elbow Point	0.0347
Synthetic JS Distance	0.1992