Strand information for cancer variants from COSMIC
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2.5 years ago

I have a very basic question. So I have downloaded somatic mutation data from the COSMIC database. Each mutation has corresponding strand information associated with them. This usually coincides with the coding strand of the gene in which the mutation is located. The strand information goes like "+" or "-". Now I want to include flanking bases (to extract mutation signatures) from each of these variants.
Say the gene SLC26A8 has a variant (C>A) at location 123454 and strand information is negative, then that means the variant is located in the anti-sense strand, right? If that variant has to flank bases such as (ACT--> AAT), then should I consider these as the bases or should I take the complementary sequence on the sense strand (TGA --> TTA) instead.

snp genome COSMIC • 559 views
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