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Old 06-04-2014, 10:32 AM   #1
nguyendofx
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Location: CA

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Default convert CDS coordinate into genome coordinate

Hi All,

I have list of genes with CDS coordinates (e.g., c.C1843T), I like genome coordinate (e.g 1:881627-881627). Does anyone know how to get it ?

Best,
Ng
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Old 06-04-2014, 12:10 PM   #2
vivek_
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If its just a few snps and you can afford to do it manually:

https://mutalyzer.nl/positionConverter
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Old 06-07-2014, 11:59 PM   #3
nguyendofx
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Thanks vivek - It works, I've confirmed with a control. However, I can't figure out the math ? genomice_position = CDS_start + CDS_coordinate_of_a_variant !
Do you have an idea how it work ?
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Old 06-08-2014, 02:57 AM   #4
gringer
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You have to do a bit more than just the location of the CDS start. If a gene has multiple exons, then you have to make sure that the position is based on the location at that exon start, rather than the start of the entire coding sequence. You also have to consider reverse complement annotations, which mess with all the numbers again.
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