masking specific regions during mapping

[dpryan]

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".

[Giles]

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?

[dpryan]

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

[Giles]

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.