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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Nope. You could simply N-mask those regions, but that will likely lead to biased mapping. -
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?Comment
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True, I just wanted to ensure that you'd thought through thatOriginally posted by Giles View Post
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".Comment
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The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
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