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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Originally posted by Giles View Postwith 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?
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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