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  • SNPs_analysis

    Dear all, I have 2 draft genomes of bacteria assembled by velvet and I used Mauve to extract snps (but I need your advice to:
    - know if these snps are synonomas or nonsynonomas
    -in which genes they are located?

    is there a softwrae that can do this?

    (I know snpeff- can be used but I do not have a reference strain)

    your advice is very appreciated

  • #2
    First you need to create an annotation (RAST) and after that you can use snpeff.

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    • #3
      thanks- have created the annotation using RAST on the draft genome- now how to us the annotation file in snpeff (can I download the genbank file to snpeff database)???

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      • #4
        This is a pain. To add a custom genome to SnpEff you need to add lines to the snpEff.config file. There is good documentation here:



        Under building databases. It is a little picky.

        i added lines to snpEff.config like this:

        #Friend Murine Leukemia Virus
        X02794.genome : FMuLV

        cd PATH/TO/snpEff/data
        mkdir X02794
        cp PATH/TO/GENBANKFILE/genes.gb X02794/genes.gb

        java -jar snpEff.jar build -genbank -v X02794

        I think that is what i did...Anyway, documentation is pretty good. I remember having a problem with my generated .gb file. Turns out there needed to be a couple of spaces after ORIGIN and the sequence.

        good luck
        --Please take everything thing I say with a grain of salt, because, if grad school has taught me anything, it's that I'm an idiot--

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