User: adakoury

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adakoury0
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Posts by adakoury

<prev • 13 results • page 1 of 2 • next >
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Comment: C: SNiPlay3: a web application to analyze VCF files
... I tried to filter for SNPs in exon regions but I got 0 results. What could be wrong? ...
written 2.5 years ago by adakoury0
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How to select envely distributed SNP markers?
... I have around 350K SNP markers from GBS. I want to select a subset of SNPs that are evenly distributed. for example 1 SNP per 50 Kb for structure analysis. Any suggestions or recommended software? Thanks Salam ...
snp written 2.5 years ago by adakoury0 • updated 2.5 years ago by genomax78k
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Comment: C: Varriant Annotation-exporting results
... Sorry I did not get the second part of the question " Also are you about the given location G:/mydata.txt is existing ?" I changed to my working directory (K drive) but did not help > rd <- rowRanges(vcf) > loc <- locateVariants(rd, txdb, CodingVariants()) 'select()' retur ...
written 2.9 years ago by adakoury0
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Varriant Annotation-exporting results
... I want to export my variant annotation results to a table and save it in my computer hard drive. I tried this "write.table(mydata, "G:/mydata.txt", sep="\t")" but did not work. ...
R snp written 2.9 years ago by adakoury0 • updated 2.9 years ago by genomax78k
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Comment: C: Variant Annotation in R
... I solved the problem. there was an error in the gff file. ...
written 2.9 years ago by adakoury0
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Comment: C: Variant Annotation in R
... I did. Is it readable now? ...
written 2.9 years ago by adakoury0
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Comment: C: Variant Annotation in R
... Which text do you refere to? ...
written 2.9 years ago by adakoury0
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Comment: C: Variant Annotation in R
... Here is the whole process. The outcome was not something I was expecting. Any idea where I amde a mistake or missed something. > vcf <- readVcf("chroA01.vcf", "Brassica_napus.annotation_v5_sorted_modified.gff") > vcf class: CollapsedVCF dim: 11847 189 rowRanges(vcf): ...
written 2.9 years ago by adakoury0
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Variant Annotation in R
... I am trying to perform Variant Annotation using "VariantAnnotation" in R I was trying to make TxDb file form Gff file but I got a warning messages as shown below. I am wondering if anybody has gone into the same problem and how it was solved. > txdb <- makeTxDbFromGFF(gtffile, format= ...
R snp written 2.9 years ago by adakoury0
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Comment: C: SNP annotation using R package
... Here what I did and what I got > library("VariantAnnotation") > vcf <- readVcf("all.filtered.recode.vcf", "Brassica_napus.annotation_v5_sorted_modified.gff") > vcf class: CollapsedVCF dim: 173864 189 rowRanges(vcf): GRanges with 5 metadata columns: paramR ...
written 2.9 years ago by adakoury0 • updated 2.9 years ago by WouterDeCoster43k

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