Question: Gene symbol list
0
gravatar for Siavash Salek Ardestani
2.2 years ago by

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

snp chip-seq next-gen sequence • 593 views
ADD COMMENTlink modified 2.2 years ago by Alex Reynolds30k • written 2.2 years ago by Siavash Salek Ardestani20

See this post, it may help.

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

ADD REPLYlink written 2.2 years ago by natasha.sernova3.7k
2
gravatar for Alex Reynolds
2.2 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

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.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Alex Reynolds30k
1
gravatar for cpad0112
2.2 years ago by
cpad011213k
India
cpad011213k wrote:

intersect with bedtools.

ADD COMMENTlink written 2.2 years ago by cpad011213k
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