Question: How to get flanking exon coordinate based on gencode gtf/gff or biomart
gravatar for ZheFrench
3.4 years ago by
ZheFrench310 wrote:

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="")

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...

gencode gff biomart annotation gtf • 1.2k views
ADD COMMENTlink written 3.4 years ago by ZheFrench310
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