User: kylvalda

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kylvalda0
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Posts by kylvalda

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biomaRt changed host issues
... Biomart has recently changed its server from www.biomart.org to www.ensembl.org This leads to the following when loading the package: > library(biomaRt) > listEnsembl() [1] biomart version <0 rows> (or 0-length row.names) > a month ago everything was fine: > listEnsembl()      ...
biomart written 3.3 years ago by kylvalda0 • updated 3.3 years ago by James W. MacDonald50k
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Answer: A: easyRNAseq annotation file
... Might this be the problem:   > annotParam<-AnnotParam(datasource=system.file('extdata','~/Homo_sapiens/Homo_sapiens/Ensembl/GRCh37/Annotation/Archives/archive-2014-05-23-16-03-55/Genes/genes.gtf')) > annotParam AnnotParamCharacter object set to retrieve 'gff3' formatted annotation from: ...
written 3.9 years ago by kylvalda0
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Answer: A: easyRNAseq annotation file
... Same problem with iGenome: Homo_sapiens/Ensembl/GRCh37/Annotation/Archives/archive-2014-05-23-16-03-55/Genes/genes.gtf ========================== Processing the annotation ========================== Validating the annotation source Read 993 records Error in .validate(obj, verbose = verbose) :   Th ...
written 3.9 years ago by kylvalda0
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Answer: A: easyRNAseq annotation file
... Hey Nico,   sorry for the late reply (am currently battling kallisto/sleuth):   > sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago) locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C ...
written 3.9 years ago by kylvalda0
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easyRNAseq annotation file
... Hi, Apparently I need to use a gtf or gff3 file for annotation with easyRNAseq now when processing hg19 bamfiles now - as method biomaRt uses GRCh39 and I get an error. So far so bad. However, I seem not to be able to download a gtf or gff3 file for hg19 that easyRNAseq would accept: > DGE< ...
annotation easyrnaseq written 3.9 years ago by kylvalda0
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package ‘BSgenome.Hsapiens.UCSC.hg38’ is not available (for R version 3.1.2)
... Hi,   trying to install package ‘BSgenome.Hsapiens.UCSC.hg38’ on R version 3.1.2.: either biocLite('BSgenome.Hsapiens.UCSC.hg38') or biocLite('BSgenome.Hsapiens.UCSC.hg38', dep=T, INSTALL_opts=c('--no-lock')) creates 23 warnings: There were 23 warnings (use warnings() to see them) > war ...
bsgenome r version 3.1.2 hg38 written 4.0 years ago by kylvalda0 • updated 4.0 years ago by James W. MacDonald50k

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Popular Question 3.3 years ago, created a question with more than 1,000 views. For package ‘BSgenome.Hsapiens.UCSC.hg38’ is not available (for R version 3.1.2)

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