How to get the gene name/region from a list of positions
I have a list of SNP positions:
761155
4402247
472711
4027247
2867693
I have a gff reference annotation file and a reference fasta file.
How do I simply find the gene name and locus (e.g. "ctpJ", "Rv3743c", respectively; or "Rv3760", "Rv3760" if there is no gene name) where these SNPs occur?
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aroso491 •
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Luther_Blisset •
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Luther_Blisset •
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Seems like you're looking for the Variant Effect Predictor. The link I've provided is for Mycobacterium_tuberculosis, which is what I presume you want based on the gene name provided. The tool works for any genome in Ensembl though.
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jared.andrews07
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Position data should include both chromosome and position within chromosome. Once you have that, you can use biomaRt to get gene data. Please search the site - that topic has been addressed multiple times.
If your list is just that, I would use http://www.ensembl.org/info/genome/variation/index.html and just check them by adding "rs" in front of each number.
How does adding
rsturn these into human mutations? As jared points out, the gene names are bacterial.I'm moving your answer to a comment until this is addressed.