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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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