Convert Chromosome postion to gene symbol
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mbansal • 0
@09b1164e
Last seen 9 months ago
United States

I am trying to find modifications in genomic location. Now, the output I am getting is in the chromosome and location of the modification (attached file). I am not sure how to convert it into a gene name using biomart or any other tool. Would you mind if you please helping me in fixing this issue? Here I don't have a range of base pairs. However, as shown below, I have just a position number in a particular chromosome number. enter image description here

biomaRt ensembldb • 793 views
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What species? What genome build? Do you only want the gene if the variant is within the gene, or close? And if 'close', how far is 'close enough'?

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It's human data. Hg19 assembly. I only want the gene if the variant is within the gene.

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Vince Schulz ▴ 150
@vince-schulz-3553
Last seen 2 days ago
United States

You could convert your information to GRanges, and then use annotatePeak from the ChIPseeker package. You can then filter the output based on which genomic region type your variants are in.

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