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Official gene symbol list to BED file

Simply trying to generate an annotated bed file for a specific assembly only from a list of official gene symbols, in my case derived from DESeq2 results. Is there a pretty straightforward way to go about doing this?

bed gene symbol deseq2
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updated by nathan bowen • nathan bowen • written by rbronste rbronste

on a Mac need a space between -v and OFS -v OFS=

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written by nathan bowen • nathan bowen

1 answer

You could get HGNC symbols via RefGene (e.g., hg38):

$ wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/refGene.txt.gz \
  | gunzip -c - \
  | awk -v OFS="\t" '{ if (!match($13, /.*-[0-9]+/)) { print $3, $5, $6, $13, ".", $4; } }' - \
  | sort-bed - \
  > refGene.hg38.sorted.bed

The sort-bed tool is via BEDOPS.

Once you have this, you could do bedops or grep operations on differentially-labeled genomic regions or gene names, resp.

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written by Alex Reynolds Alex Reynolds

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