Intro to Genomic Features
https://www.dominodatalab.com/blog/genomic-ranges-an-introduction-to-working-with-genomic-data https://bioconductor.org/packages/release/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.html https://www.dominodatalab.com/data-science-dictionary/genomicranges
I've been trying to use Julia more for some tertiary analysis of genomic data. It seems that BioJulia has a package for every bioinformatics format created, so far. However, I've been missing the supplementary blog posts that show you the real world use of these packages. Or maybe something like the great documentation PyRanges has.
Downloading our data
using Downloads
if !isfile(raw"H3K27ac.consensus_peaks.bed")
Downloads.download("https://utdallas.box.com/shared/static/y4glk8y8chjq5fuv6iowe6bjz1vovkr3.bed", "H3K27ac.consensus_peaks.bed")
Downloads.download("https://utdallas.box.com/shared/static/y4glk8y8chjq5fuv6iowe6bjz1vovkr3.bed", "p63_4A4.consensus_peaks.bed")
end
Find overlaps
So you want to find some overlaps?
using GenomicFeatures
using BED
# Create an interval collection in memory.
h3k27ac_icol = open(BED.Reader, "H3K27ac.consensus_peaks.bed") do reader
IntervalCollection(reader)
end
p63_icol = open(BED.Reader, "p63_4A4.consensus_peaks.bed") do reader
IntervalCollection(reader)
end
overlap_icol = eachoverlap(h3k27ac_icol, p63_icol)
overlaps = collect(overlap_icol)
overlaps