Open chromatin assays show distinct fragment length enrichments, as the cut
sites are only in open chromatin and not in nucleosomes. As such, peaks
representing different n-nucleosomal (ex mono-nucleosomal, di-nucleosomal)
fragment lengths will arise. Good libraries will show these peaks in a
fragment length distribution and will show specific peak ratios.
NFR: Nucleosome free region
Sequence quality metrics (filtered/deduped BAM)
rep1
Open chromatin assays are known to have significant GC bias. Please take this
into consideration as necessary.
Annotated genomic region enrichment
rep1
Fraction of Reads in universal DHS regions
0.3976051749771341
Fraction of Reads in blacklist regions
0.028447338422676445
Fraction of Reads in promoter regions
0.17322362748943085
Fraction of Reads in enhancer regions
0.3065149606248619
Signal to noise can be assessed by considering whether reads are falling into
known open regions (such as DHS regions) or not. A high fraction of reads
should fall into the universal (across cell type) DHS set. A small fraction
should fall into the blacklist regions. A high set (though not all) should
fall into the promoter regions. A high set (though not all) should fall into
the enhancer regions. The promoter regions should not take up all reads, as
it is known that there is a bias for promoters in open chromatin assays.
Replication quality metrics
Number of raw peaks
rep1
Number of peaks
298799
Top 300000 raw peaks from macs2 with p-val threshold 0.01
Peak calling statistics
Peak region size
rep1
Min size
150.0
25 percentile
301.0
50 percentile (median)
529.0
75 percentile
898.0
Max size
3326.0
Mean
651.4975083584617
rep1
Enrichment / Signal-to-noise ratio
Jensen-Shannon distance (filtered/deduped BAM)
rep1
AUC
0.2132944816003156
Synthetic AUC
0.49732089527159934
X-intercept
0.11318959226717046
Synthetic X-intercept
0.0
Elbow Point
0.7731749982507172
Synthetic Elbow Point
0.5009103768028452
Synthetic JS Distance
0.4197847791033767
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for macs2 raw peaks
rep1
Fraction of Reads in Peaks
0.31969829236908587
For macs2 raw peaks:
repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)
For overlap/IDR peaks:
repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates
