convert CDS coordinate into genome coordinate

nguyendofx · 06-04-2014, 11:32 AM

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

vivek_ · 06-04-2014, 01:10 PM

If its just a few snps and you can afford to do it manually:

https://mutalyzer.nl/positionConverter

nguyendofx · 06-08-2014, 12:59 AM

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 ?

gringer · 06-08-2014, 03:57 AM

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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06-04-2014, 11:32 AM	#1
nguyendofx Member Location: CA Join Date: May 2011 Posts: 31	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

06-04-2014, 01:10 PM	#2
vivek_ PhD Student Location: Denmark Join Date: Jul 2012 Posts: 164	If its just a few snps and you can afford to do it manually: https://mutalyzer.nl/positionConverter

06-08-2014, 12:59 AM	#3
nguyendofx Member Location: CA Join Date: May 2011 Posts: 31	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 ?

06-08-2014, 03:57 AM	#4
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 838	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.