User: AGE

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AGE20
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Posts by AGE

<prev • 15 results • page 2 of 2 • next >
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how to compute Dxy using pool-seq frequency data.
... I'm wondering how Dxy is computed using allele frequency data from pool-seq. For example here: > "Allele frequencies based on SNPs were estimated with > snp-frequency-diff.pl, filtering with the same thresholds a described > for FST estimates. We computed the measure of divergence DXY f ...
genome R snp written 6 months ago by AGE20
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Software for finding age of mutation
... I'm trying to find methods that find the age of a mutation or haplotype, using LD or anything else. So far I've only found this: http://bioinf.wehi.edu.au/software/ageofmutation/ But I'm wondering if there are any other methods. ...
software R next-gen written 6 months ago by AGE20 • updated 6 months ago by zx87548.2k
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Comment: C: Blasting an assembly against a single gene of interest
... Of that's right! I'll try that, thanks! ...
written 7 months ago by AGE20
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Blasting an assembly against a single gene of interest
... I have two genome assemblies for one species that is polymorphic with respect to colour and a list of genes of interest. I want to extract the contigs from each assembly that map to a gene of interest, call it gene X. The way I was thinking of doing this, is by blasting the each assembly against ...
gene assembly next-gen blast genome written 7 months ago by AGE20 • updated 7 months ago by h.mon27k
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--min-count of popoolation2 (the minimum count of the minor allele)
... Can someone explain how the --min-count for the minor allele works in popoolation2? The default is 2 but I am not sure what that translates to when it comes to frequency and it also seems low. If I have two pools of 50 individuals each, does that mean that --min-count 5 would translate to MAF of 0. ...
popoolation2 next-gen snp written 10 months ago by AGE20

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