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  • masking specific regions during mapping

    Is there a way to provide Bowtie2 (or BWA) with a file containing specific regions of the genome to ignore during mapping? I can't find such a command line argument in the manual, but I've missed such things before.

  • #2
    Nope. You could simply N-mask those regions, but that will likely lead to biased mapping.

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    • #3
      with repeats, there is no way around bias. Its just choosing which bias is the closest to the truth. anyway, how can you N-mask within bowtie?

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      • #4
        Originally posted by Giles View Post
        with repeats, there is no way around bias. Its just choosing which bias is the closest to the truth. anyway, how can you N-mask within bowtie?
        True, I just wanted to ensure that you'd thought through that

        You can't do that within bowtie, but you can make a bed file of the regions to be masked and then use "bedtools maskfasta".

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