User: Didi

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Didi10
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4 days, 12 hours ago
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1 year, 2 months ago
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Posts by Didi

<prev • 22 results • page 1 of 3 • next >
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Comment: C: VariantAnnotation: Error with ScanVcfParam
... It's working.  Thanks a lot.   ...
written 13 days ago by Didi10
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Comment: A: VariantAnnotation: Error with ScanVcfParam
... Hi, I checked and everything seems ok. headerTabix(tab)$seqnames [1] "Chr1" "Chr2" "Chr3" "Chr4" "Chr5" "Chr6" "Chr7" "Chr8" "Chr9" "Chr10" [11] "Chr11" "Chr12" I still don't know what's the problem. ...
written 13 days ago by Didi10
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VariantAnnotation: Error with ScanVcfParam
... Hi, I tried to get from the VCF file the SNPs that are in chr5 between 3-6Mb using this script and I've got this error. library(VariantAnnotation) library(Rsamtools) VARvcf <- readVcf("/media/Data/VAR_reads (Variants).vcf.gz") idx <- indexTabix("/media/Data/VAR_reads (Variants).vcf.gz", "vcf ...
variantannotation vcf readvcf filtervcf scanvcfparam written 13 days ago by Didi10
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Answer: A: add annotation features to BSgenome or txdb package
... I have GTF and GFF files. I imported them as a TxDb object and it works. Thanks a lot. Regards, D. ...
written 20 days ago by Didi10
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add annotation features to BSgenome or txdb package
... Hi,  Is it possible to add annotation features to a BSgenome package or a txdb package in case there isn't an orgDB package for non model organisms? Is it easy to do it? Thanks a lot.  Regards, D. ...
annotation bsgenome orgdb txdb written 26 days ago by Didi10
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Answer: A: Cytoband information for rice
... Thanks a lot.  Regards, D.   ...
written 27 days ago by Didi10
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Cytoband information for rice
... Hi, Does anyone know from where getting the cytoband information for rice (Oryza sativa) to draw the ideogram for a circular visualization? Thanks a lot. Regards, D. ...
ideogram ggbio rice cytoband circlize written 6 weeks ago by Didi10
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Answer: A: BiomaRt package not working
... Thank you so much. It's working now by using : go <- getBM(attributes = c("go_id", "tair_locus", "namespace_1003"),              mart=ensembl) It was really helpful. Thanks again.   ...
written 3 months ago by Didi10
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Comment: C: BiomaRt package not working
... Thanks a lot.  ...
written 3 months ago by Didi10
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BiomaRt package not working
... Hi, I usually use this script to get the GO IDs but I'm getting the error below since yesterday. library("biomaRt") listMarts(host="plants.ensembl.org")  m <- useMart("plants_mart", host="plants.ensembl.org"); listDatasets(ensembl) ensembl= useDataset("athaliana_eg_gene", mart=ensembl) go < ...
biomart getbm written 3 months ago by Didi10

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