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Report generated at 2022-01-15 11:43:47

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	64939380	98701132
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	57484465	96181840
Mapped(QC-failed)	0	0
% Mapped	88.5200	97.4500
Paired	64939380	98701132
Paired(QC-failed)	0	0
Read1	32469690	49350566
Read1(QC-failed)	0	0
Read2	32469690	49350566
Read2(QC-failed)	0	0
Properly Paired	56459515	77055364
Properly Paired(QC-failed)	0	0
% Properly Paired	86.9400	78.0700
With itself	56970645	94971565
With itself(QC-failed)	0	0
Singletons	513820	1210275
Singletons(QC-failed)	0	0
% Singleton	0.7900	1.2300
Diff. Chroms	280838	14544721
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	26183407	34047307
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	8391550	359515
Paired Opt. Dupes	3135	1894
% Dupes/100	0.3205	0.0106

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	26180810	34044272
Distinct Read Pairs	17790091	33684905
One Read Pair	11823780	33341128
Two Read Pairs	4246324	333429
NRF = Distinct/Total	0.6795	0.9894
PBC1 = OnePair/Distinct	0.6646	0.9898
PBC2 = OnePair/TwoPair	2.7845	99.9947

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	35583714	67375584
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	35583714	67375584
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	35583714	67375584
Paired(QC-failed)	0	0
Read1	17791857	33687792
Read1(QC-failed)	0	0
Read2	17791857	33687792
Read2(QC-failed)	0	0
Properly Paired	35583714	67375584
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	35583714	67375584
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	49924
Np	0
N optimal	49924
N conservative	49924
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.	170
Corr. Est. Fragment Len.	0.2842
Phantom Peak	55
Corr. Phantom Peak	0.2063
Argmin. Corr.	1500
Min. Corr.	0.1428
NSC	1.9904
RSC	2.2275

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	0.6806

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	0.0670
AUC	0.4932
CHANCE divergence	0.3893
Elbow Point	0.0000
JS Distance	0.9011
Synthetic AUC	0.4969
Synthetic Elbow Point	0.5510
Synthetic JS Distance	0.6455