Hello,
I'm looking at population level variation in a 100kb region in Drosophila. When I use standard alignment programs (bwa and bowtie) on reads from some sequenced populations, I keep losing insertions that I know are present (and appear in the raw reads), but are missing in the reference genome.
Someone suggested I do a denovo assembly on my 100kb region (since I'm not really interested in the rest of the genome), to get around this problem.
Is there a way to filter reads for a specific region using denovo assembly? Is this a good approach to the problem, or am I better off tweaking my methods with alignment to the reference genome?
Thanks!
I'm looking at population level variation in a 100kb region in Drosophila. When I use standard alignment programs (bwa and bowtie) on reads from some sequenced populations, I keep losing insertions that I know are present (and appear in the raw reads), but are missing in the reference genome.
Someone suggested I do a denovo assembly on my 100kb region (since I'm not really interested in the rest of the genome), to get around this problem.
Is there a way to filter reads for a specific region using denovo assembly? Is this a good approach to the problem, or am I better off tweaking my methods with alignment to the reference genome?
Thanks!
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