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3.1 years ago
shpak.max
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50
I have a list of SNP coordinates of interest based on a study that used Drosophila reference genome 5.18. I would like to compare these to some data that we have based on a different reference genome (5.57).
What would be the most efficient way to convert the coordinates based on one reference to the latter reference genome?
What kind of comparison are you looking to do e.g. if they are in the same gene/location? You may want to use
crossmap
(LINK) to lift one of the results over and then do the comparison w.r.t the same genome. Additional tools here.Basically, if something is at site 100000 on Chromosome 2L based on the author's reference genome, I want to know the equivalent coordinate using my reference genome.