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
0.3757864734364721
Fraction of Reads in blacklist regions
0.011081822907952153
Fraction of Reads in promoter regions
0.16078138522648178
Fraction of Reads in enhancer regions
0.29763403180544307
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
273184
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
192.0
50 percentile (median)
291.0
75 percentile
522.0
Max size
2888.0
Mean
410.15737378470186
rep1
Enrichment / Signal-to-noise ratio
Jensen-Shannon distance (filtered/deduped BAM)
rep1
AUC
0.2079560276686515
Synthetic AUC
0.49389598152045744
X-intercept
0.1424946917623349
Synthetic X-intercept
4.5390280401593905e-230
Elbow Point
0.7120975836022441
Synthetic Elbow Point
0.5052097740939918
Synthetic JS Distance
0.40326931474248706
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for macs2 raw peaks
rep1
Fraction of Reads in Peaks
0.28711961470626496
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
