Questions tagged [radseq]

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Comparing loci across catalogs

Context: I'm using the Stacks (v2.59) ref_map.pl command to analyze garden and wild samples of a plant species, and have aligned my paired-end RAD reads to a reference genome (using GSNAP). The goal ...
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Combine two alleles to genotype locus?

I have a following fasta (produced by stacks populations): ...
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2 answers
106 views

Denovo, Stacks: Getting an “ambiguous redirect” error

I tried running the following command ...
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1 vote
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170 views

GBS: clustering of PCoA axes with R package mclust to describe identity by missingness

I have a SNP dataset with 56 populations and 430 samples that was produced by GBS sequencing. I need to identify groups of samples that have similar patterns of genotype missingness, since there is ...
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2 votes
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R package grur: missing_visualization() fails during redundancy analysis of .vcf

I am trying to use the R package grur to process GBS SNP data, which is installed from github as instructed. For starters, I am running the test code in this vignette. As suggested I am running it ...
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2 votes
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141 views

Post ipyrad filtering of SNP loci from GBS, based on SNP quality

I want to use SNPs produced by Ipyrad, which is a python script for RADseq, using maize genome data via RAxML to examine the monophyly of a highly-variable focal species and its phylogenetic ...
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4 votes
1 answer
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Make ipyrad use cuda-enabled NVidia card on Ubuntu

I want to use ipyrad on a new Ubuntu machine that has an NVidia Quadro K2000 card with 384 cores. One can configure ipyrad to run on a linux cluster. Do I have any options to get ipyrad to access ...
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1 answer
108 views

Why do reverse radtags have different start points in radtag sequencing?

Why is it that when doing paired end Radseq that R1 and R2 have different start points? For instance, while doing Radseq you do a restriction digestion of your DNA using enzyme X- shouldn't the ...
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Assembling sequence data generated by RADseq [closed]

I'm working on a project where I have to assemble sequences generated by RADseq. At the end I hope to compare two species of woodpeckers in Sri Lanka by using SNPs. I tried to assemble it using ...
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