Maybe naïve question, but I was wondering, when you are looking to a specific exon of interest :
How do you get previous and next exon coordinates. Is there a simple way to extract that from the gtf file or biomart in R/python ?
Most of the time I'm working with R , and I import my annotations using biomart or saved Txdb object.
txdb <- loadDb("/home/jean-philippe.villemin/gencode.v25.annotation.sqlite") edb = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",host="jul2016.archive.ensembl.org")
So if my exon coordinates are given as follows chr17:64,502,023-64,502,086, how to get coordinates for exon N-1/N+1 without using transcript spurious name...