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  • dpryan
    replied
    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".

    Leave a comment:


  • Giles
    replied
    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?

    Leave a comment:


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

    Leave a comment:


  • Giles
    started a topic masking specific regions during mapping

    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.

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