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User: kristenbeck527

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Posts by kristenbeck527

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Comment: C: customProDB: issues getting dbSNP data for non-model organism
... Great! Will do. Thank you.  ...
written 3.6 years ago by kristenbeck5270
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Comment: C: customProDB: error aberrant fasta from indels
... Excellent! It worked. Thank you.   ...
written 3.6 years ago by kristenbeck5270
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Comment: C: customProDB: error aberrant fasta from indels
... Here is my session info: > sessionInfo() R version 3.1.3 (2015-03-09) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.4 (Yosemite) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats4    parallel  stats     graphics ...
written 3.6 years ago by kristenbeck5270
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customProDB: error aberrant fasta from indels
... I am trying to make a variant called fasta file using CustomProDB. I am able to generate the SNV fasta but running into issues generating the indel derived fasta. Steps related to generating the aberrant fasta: vcf = InputVcf(vcffile) index <- which(values(vcf[[1]])[['INDEL']]==TRUE) # returns ...
variantannotation indel fasta customprodb written 3.6 years ago by kristenbeck5270 • updated 3.6 years ago by xiaojing.wang50
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Comment: C: customProDB: issues getting dbSNP data for human (hg19)
... Thank you for your response! It worked with "snp138" and your code provided helped me to better understand the genome in this session. ...
written 3.6 years ago by kristenbeck5270
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customProDB: issues getting dbSNP data for human (hg19)
... I am trying to use the variant annotation capabilities in customProDB. I would like to make a variant annotated fasta file, but I am running into issues retrieving the dbsnp data for hg19. PrepareAnnotationRefseq(genome='hg19', CDSfasta, pepfasta,   annotation_path=annotation_path_hs, splice_m ...
varianttools dbsnp customprodb refseq written 3.6 years ago by kristenbeck5270 • updated 3.6 years ago by xiaojing.wang50
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Comment: C: customProDB: issues getting dbSNP data for non-model organism
... Thank you for your reply! Do you have any suggestions on converting the Biomart table to the expected Granges format that the subsequent functions are expecting? ...
written 3.6 years ago by kristenbeck5270
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customProDB: issues getting dbSNP data for non-model organism
... I'm trying to use PrepareAnnotationEnsembl() function in customProDB. Based on Ensembl's site the current dbSNP version for Macaca mulatta is snp131. However, if I try to enter that into the function I get an error. ensembl = useMart(biomart="ensembl") ensembl = useMart("ENSEMBL_MART_ENSEMBL", dat ...
ensembl dbsnp macaque customprodb written 3.6 years ago by kristenbeck5270 • updated 3.6 years ago by xiaojing.wang50

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