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  • mapper which work with ambiguous bases

    hello,

    which (RNA-seq) mappers can use ambiguous bases in the reference genome?
    -STAR
    -subread
    -RUM
    -tophat


    ambigous bases are e.g.
    W for A,T
    S for G,C
    Y for C,T
    B for non-A
    ...

    and is there a script which can use a SNP dataset and modify the genome accordingly: replace all SNP positions with the correct ambiguous bases?

    dietmar

  • #2
    Tophat/Bowtie works with 'N' (i.e. any base), and I think any non-ACGTU are converted to Ns. To accept all ambiguous bases in a DNA database, you need to double the minimum number of bits used to 4 (i.e. presence/absence of each base). The search algorithms also need to change quite a bit, which will probably at least double the time taken. I'm not yet convinced the added complexity is worth it.

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    • #3
      Gsnap can map to a genome with SNPs though I don't think it takes the exact input type you have in mind.

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