Gene symbol list

Question

[Siavash Salek Ardestani]

Hi, I have many coordinates (approximatly1000), I want to know how can I find the gene symbols that are in these coordinates? Thanks, Siavash

[natasha.sernova]

See this post, it may help.

Is There An Easy Way Of Getting Gene Symbols From Genomic Coordinates?

Answer 1

[Alex Reynolds]

You can use BEDOPS bedmap --echo-map-id-uniq to map IDs from a BED file of gene annotations to a list of intervals-of-interest:

$ bedmap --echo --echo-map-id-uniq coordinates.bed genes.bed > answer.bed

You will provide the sorted BED file coordinates.bed.

To generate genes.bed, this will depend on your organism and reference genome. Here's an example of how to get this file for human hg38:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.annotation.gff3.gz \
    | gunzip -c - \
    | awk '$3 == "gene"' - \
    | convert2bed -i gff - \
    | awk -vOFS="\t" '{ match($0, /gene_name=(.*);level/, a); $4=a[1]; print $0; }' - \
    > genes.bed

Going back to the bedmap --echo-map-id-uniq command, the file answer.bed will have each coordinate from coordinates.bed, and the HGNC symbol names of Gencode v27 gene annotations that overlap those coordinates.

Answer 2

[cpad0112]

intersect with bedtools.