AA position to genomic location
Hi!
I have a big list of mutated amino acid positions, for each mutation I also have the related gene. I would like to end up with a bed file with all chromosome locations for each mutation. Given a position of an Amino acid, how can I get the chromosome location?
Example:
input:
Amino acid Gene
54 EGFR
output:
chr start end Gene
1 1234 1235 EGFR
I tried by multiply the length of the coding region of the gene by the Aa position. I realized that this is not correct as I'm not assuming the introns...
thanks in advantage
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xcalle91 •
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That's not a straightforward problem. I assume you know the isoform in which this counting is performed?
duplicate of Amino Acid Change To Genomic Location
Hello xcalle91!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
PS: Pierre's backlocate is one of the best command line tools for the task