[mira_talk] Re: highly heterozygous assembly
- From: Adrian Pelin <apelin20@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Sat, 16 Aug 2014 12:31:17 -0400
Hello mira_talk,
I sent an email a few days ago attached below about highly heterozygous
assemblies.
I was wondering if there is any way to adjust the parameters to warn
MIRA of sample variation.
I know at one point this was discussed in one of the forum emails, but I
simply cannot find the parameter in question.
Thank you all,
Adrian
On 8/10/2014 11:18 AM, Adrian Pelin wrote:
Hello,
I have analyzed my genome, and I know that about 25% of it is in a
coverage that is above average, so duplicated regions.
I also know that overall, the genome has 35 SNPs/1kb, and these are
heterozygous loci in a tetraploid, so the allele frequencies of these
are either 25% or 50%. Aside from that there are many SNPs at low
frequencies, because the data comes from multiple spores sequenced.
Any advice on tweaking the manifest file for the assembly?
Adrian
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