BED file with coding exons, the adjacent intronic region (+-20 bp) and the gene name

Question

[agonzalezdelavega]

Hi all,

I need to create a BED file with the coding exons (only coding) of all the exome genes, the adjacent intronic region (+-20 bp) and the gene name.

UCSC Genome Browser allows to download all exons with +-20 bp but not only the coding ones. And it also includes the transcript_id but not the name of the gene.

Any idea how to do this?

Thank you very much in advance.

[jv]

If you are using the Table Browser, under the Select Data section there is a drop down list for "table" and there are a number of options available for refining which annotations are returned that are relative to the "track" that is selected.

For example, for "track" GENCODEV41 (for assembly GRCh38) you can select "table" knownCds which should include only know coding sequences.

If you looking through the different options available for refining your Table Browser settings you should be able to find something that yields what you are looking for.