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Hi- I am using Mauve to export SNPs (but I am not sure why I get more SNPs than it is published before)- for example snps between 2 bacterial strains should be 500 but I get > 2000 snps- any advice why does this happen, please?
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when you said "published before" do you refer to previous detected SNPs using mauve or another tool?Originally posted by mmmm View Post
SNP calling can vary between tools depending on how you mask low complexity regions. -
thank you very much for clarification- so do I mask low complexity regions using Mauve??Comment
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Honestly I don't know, I'm not familiar with mauve algorithm.
have you tried with Mummer 3? http://mummer.sourceforge.net
I know Mummer can mask LCR.Comment
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thanks- I am using Mauve at the moment, any one could explain getting many snps than actual snps using mauve? (any parametes should be adjusted)?Comment
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