27 days ago by
Any BED or interval dataset can be compared with another to find common regions of overlap if the coordinates are based on the same reference genome.
UCSC can be a good source for reference annotation in BED format. If you have gene names/symbols those can be used as filtering criteria when extracting data from a track. Or you can select all of the promoter, exon, intron (and other features, as available) for all genes/transcripts in a track and compare from there, link in identifiers (gene names), and perform downstream analysis/graphing.
Several Galaxy tutorials cover methods to do this type of analysis: https://galaxyproject.org/learn/
Start here with the 101, which shows the simplest way to directly compare two bed/interval datasets to find common regions:
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Hope that helps! Jen, Galaxy team