Retrieve exon positions from UCSC Genome Browser
Title says it all. I'm interested in a specific gene, say HK1. How can I retrieve the exon positions?
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You could use rtracklayer in R:
library(rtracklayer)
ucsc <- browserSession()
query <- ucscTableQuery(ucsc, "knownGene", names="HK1")
HK1 <- track(query)
HK1.tx <- blocks(HK1)
This yields a GRangesList object, where each element contains the exon ranges for one of the 7 trancripts for HK1.
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