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  • Reduced Representation Library construction for SNP discovery

    Hi,

    I am preparing to go for SNP discovery in a plant genome by constructing reduced representation libraries. I already have quite a few published papers for reference. However, I would be grateful if anyone could suggest a working protocol for selection of a suitable Restriction Enzyme (meth-sensitive or meth-insensitive) for an entire genome and for constructing an RRL using the same RE.

    Thank you in advance.

  • #2
    RAD Wiki

    Have you had a look at the RADSeq Wiki?
    https://www.wiki.ed.ac.uk/display/RADSequencing/Home

    There is a working protocol for library prep there and an Excel spreadsheet for selecting enzymes based on genome size, GC content and predicted number of enzyme cut sites.

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    • #3
      Thank you very much Uranotaenia! I will check this link out and let you know if it helps.

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      • #4
        RRL sequence -unique SNP calling in unaligned regions.

        Hi, we have a prepared library of RRL sequences for the an un-assembled genome (tetraploid). the region of interest is 250 bases long, sequenced 72 BP single end. We are using 1 of its parent genome as a partial reference. We also need to call the SNPs from the region which has not been aligned to our partial reference genome??? can some 1 suggest some tools that will help in the downstream analysis.

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