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
0.3815631046283398
Fraction of Reads in blacklist regions
0.0037620614546766463
Fraction of Reads in promoter regions
0.1705001557206189
Fraction of Reads in enhancer regions
0.3124610075287143
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
298730
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
259.0
50 percentile (median)
467.0
75 percentile
829.0
Max size
3453.0
Mean
620.7627255381113
rep1
Enrichment / Signal-to-noise ratio
Jensen-Shannon distance (filtered/deduped BAM)
rep1
AUC
0.20159970854821632
Synthetic AUC
0.4959910953972784
X-intercept
0.1212488354145924
Synthetic X-intercept
0.0
Elbow Point
0.7224348132064985
Synthetic Elbow Point
0.5048362707713107
Synthetic JS Distance
0.4227219314637703
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for macs2 raw peaks
rep1
Fraction of Reads in Peaks
0.2988726186626998
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
