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
0.5032109328753267
Fraction of Reads in blacklist regions
0.01124077776461134
Fraction of Reads in promoter regions
0.26298600044028975
Fraction of Reads in enhancer regions
0.3223609866933953
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
299114
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
496.0
50 percentile (median)
784.0
75 percentile
1134.0
Max size
3716.0
Mean
855.4477122434924
rep1
Enrichment / Signal-to-noise ratio
Jensen-Shannon distance (filtered/deduped BAM)
rep1
AUC
0.13254289754636286
Synthetic AUC
0.49818785741163524
X-intercept
0.1226548255014235
Synthetic X-intercept
0.0
Elbow Point
0.8004202520712709
Synthetic Elbow Point
0.49844665077445394
Synthetic JS Distance
0.5588497693477705
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for macs2 raw peaks
rep1
Fraction of Reads in Peaks
0.45724388270374006
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
