Quick And Easy Way To Find Whether A Locus Is Falling In Which Region Of Exon Or Intron

Question

[skm770]

Is there an easy way to find whether a locus is falling in "start of exon" or "terminal region of exon" or in the "start of intron" or "terminal region of the intron" or "middle region of intron"

Answer 1

[Devon Ryan]

Have a look at the GenomicFeatures package in R/Bioconductor. You'll have to come up with a definition for "start" and "middle", but you could then use the various nearest() functions from GenomicRanges/IRanges to get an index of the nearest feature.