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
0.563152961981241
Fraction of Reads in blacklist regions
0.001676454564679199
Fraction of Reads in promoter regions
0.2753442601364468
Fraction of Reads in enhancer regions
0.3087347701017787
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
203291
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
277.0
50 percentile (median)
533.0
75 percentile
841.0
Max size
2782.0
Mean
606.0469081267739
rep1
Enrichment / Signal-to-noise ratio
Jensen-Shannon distance (filtered/deduped BAM)
rep1
AUC
0.13433742482095123
Synthetic AUC
0.4960203224784086
X-intercept
0.12991009038944837
Synthetic X-intercept
0.0
Elbow Point
0.8731468763557917
Synthetic Elbow Point
0.5007176925732826
Synthetic JS Distance
0.569858167571406
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for macs2 raw peaks
rep1
Fraction of Reads in Peaks
0.49598841332777277
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
