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Hello Dr. Rannala,
Is there any reason I should not use the haplotypes of RADseq loci in BA3SNP as long as I filter for
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I'm trying to load diploid genome data using the Read.DiploidFasta() function but I'm unable to do so.
It seems the function does not load the stringr package but even after loading it, it tries to…
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Dear Armando,
I have a ddRADseq dataset with about 70,000 SNPs. I ran GONE using the default parameters from the INPUT_PARAMETERS_FILE, and I double-checked to ensure that all the parameters are ap…
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Would it be useful to be able to specify your reads in text files? This would be in addition to the current thing where you can do a directory or a glob.
This could be useful if you have a whole to…
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Hello,
I have WGS sequencing data, incuding the bam files and the called SNPs as vcf. I used now stitch to impute my SNPs based on the bam files and the SNP positions. However, I realized since I am …
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Hello,
I am running psmc on RADseq data following Liu and Hansen (2017) method that prepares the RADseq data for this psmc analysis. When I run psmc on my full dataset (~1700 scaffolds ranging an…
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Hi
I m trying to insert my SNP data generated from RADseq vcf file, I have about 17000 loci and definitely many cases as such the error indicates, either for pop1 or 2 or 3.
How do you suggest I s…
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Hi,
I tried to use snpgdsLDpruning() for the first time, but I get a pruned snp dataset with no SNPs.
This is the code I used:
My dataset comes for RADseq and contains SNPs data but no chromo…
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Hi there,
I'm hoping to use locator to predict the origin of some kelp rafts i've collected. I have wide spanning RADseq data across the range of the species, and then I have 40 samples which were fo…
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Human - [1000 genomes data](https://www.internationalgenome.org/) might not be the best currently available. Or [gnomAD](https://gnomad.broadinstitute.org/downloads), which has hella more genomes. It'…