User: cav3gh

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cav3gh0
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Posts by cav3gh

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VCF file does not include snp.id, can I still run SNPRelate for Relatedness Analysis? Data is output from STACKS for mangroves
... I am using the Tutorials for the R/Bioconductor package SNPRelate trying to run a relatedness analysis. I have a VCF output file from STACKS for mangrove (*Avicennia germinans*) populations. The VCF includes the following information: INFO ID=NS,Number=1,Type=Integer,Description="Number of Sample ...
snprelate vcf written 19 days ago by cav3gh0 • updated 18 days ago by Stephanie M. Gogarten590
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Error in seqVCF2GDS FORMAT ID 'AD' should have 1 value(s), but receives 2.
... I am trying to use SNPRelate to run some data analysis on a VCF file output from STACKS. I have gotten the file to read into R, but now when I am trying to cover to GDS file I keep getting the following error: Error in seqVCF2GDS(vcf.fn, "Full_Study.gds") : FORMAT ID 'AD' should have 1 value(s), ...
seqvcf2gds written 19 days ago by cav3gh0 • updated 16 days ago by qliu70
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SNPrelate, snpgdsFst is excluding all snps on non-autosomes, how can I get it to stop doing that?
... I am trying to run a Fst on VCF file output from STACKS from DDRAD sequencing run.  The problem is that when I am running: vcf.fn <- "batch_1.vcf" snpgdsVCF2GDS(vcf.fn, "test.gds", method = "biallelic.only") snpgdsSummary("test.gds") genofile <- snpgdsOpen("test.gds") sample.id <- read.gds ...
snprelate fst written 6 months ago by cav3gh0 • updated 6 months ago by zhengx20
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Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems with vcf.fn
... So, I can read the vcf file into R using read.vcf, but I cannot seem to get seqVCF2GDS to work.  I have tried the following code: > vcf_test1 <- read.vcf("/Users/Desktop/batch_1.vcf") Reading 10000 / 10000 loci. Done. > vcf.fn <- "C:/Users/Desktop/batch_1.vcf" > seqarray_test1 <- ...
seqarray written 8 months ago by cav3gh0 • updated 8 months ago by Stephanie M. Gogarten590
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Defining populations in a msaClustalOmega alignment
... I ran the following code: mySequences <- readAAStringSet("batch_1.fa") myFirstAlignment <- msaClustalOmega(mySequences) msaPrettyPrint(myFirstAlignment, output=c("pdf", "tex", "dvi", "asis")) msaPrettyPrint(myFirstAlignment, output="asis", alFile = "/Users//Desktop/alignment.fasta") batch_1. ...
msa written 10 months ago by cav3gh0
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How to get msa output in fasta format
... My current code is : mySequences <- readAAStringSet("batch_1.fa") myFirstAlignment <- msaClustalOmega(mySequences) msaPrettyPrint(myFirstAlignment, output=c("pdf", "tex", "dvi", "asis")) msaPrettyPrint says that its first writes to a fasta file but does not include that as an output option ...
msa msaprettyprint() written 11 months ago by cav3gh0 • updated 11 months ago by UBodenhofer250
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msa output formats for use down stream to create phylogenetic trees
... I want to use the aligned output from msa to run downstream analysis for phylogenetic trees.  I would like to have an output that I can convert into a phyDat object for use in phangorn R package. pkg <- 'BiocInstaller' already_installed <- installed.packages()[ ,1] if (!(pkg %in% already_inst ...
R bioconductor phylogenetic written 12 months ago by cav3gh0

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