Question: ucsc RSid to gene name
0
gravatar for pinikoma
3.3 years ago by
pinikoma0
Israel
pinikoma0 wrote:

Hi all,

 

where can I find a table containing rsid to gene name transformation , preferably at the ucsc database ?

ucsc rsid gene • 1.9k views
ADD COMMENTlink modified 3.3 years ago by Alex Reynolds27k • written 3.3 years ago by pinikoma0
1

duplicate of How To Map A Snp To A Gene Around +/- 60Kb ?

ADD REPLYlink written 3.3 years ago by Pierre Lindenbaum118k

so you are saying that position by kb is the only way to find out what gene a snp belongs to ?, there is no special table for this ?

ADD REPLYlink written 3.3 years ago by pinikoma0
1
gravatar for Alex Reynolds
3.3 years ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k wrote:

Another way to get access to UCSC datasets and do genomic set operations is via the command line, using mysql, wget and BEDOPS tools like gtf2bed and bedmap.

Get all SNP rs* IDs via the command line:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e 'SELECT chrom, chromStart, chromEnd, name FROM snp142Common;' hg19 > snp142Common.bed

Get genes and convert to BED:

$ wget -O - ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz \
    | gunzip -c \
    | grep -w "gene" \
    | gtf2bed \
    > gencode.v19.genes.bed

Map gene names (in the gene ID field) to SNPs, using bedmap to look for SNPs whose positions overlap those of Gencode genes:

$ bedmap --echo --echo-map-id-uniq snp142Common.bed gencode.v19.genes.bed > snpsWithMappedGeneIds.bed

If you want, you can expand the window around a SNP by some number of bases to allow a looser search ("nearby" genes) by adding the --range option to bedmap.

For example, for a 1 kb window centered on each SNP, add --range 500:

$ bedmap --echo --echo-map-id-uniq --range 500 snp142Common.bed gencode.v19.genes.bed > snp1kbWindowsWithGeneIds.bed
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Alex Reynolds27k
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