candidate gene identification
Hi community, need suggestions
I have physical position of SNPs and I have to find the candidate gene near by SNPs. help to solve this problem.
e.g.:
chromosome 3 position 196643035
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2 answers
Convert your SNP positions to sorted BED3 format with awk or similar, to make a file called snps.bed.
Download annotations and convert to BED. For example:
$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_21/gencode.v21.annotation.gff3.gz \
| gunzip --stdout - \
| awk '$3 == "gene"' \
| convert2bed -i gff - \
> genes.bed
Then use closest-features to find the nearest annotation to each SNP:
$ closest-features snps.bed genes.bed > answer.bed
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Use the UCSC genome browser. Explore it, and you can visualize multiple factors in context.
In other news, you really need to learn how to phrase your questions well.
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