User: josev.die

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josev.die10
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Posts by josev.die

<prev • 5 results • page 1 of 1 • next >
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Answer: A: How do I make this perl script work to fetch sequences from NCBI using gene symb
... If you are open to use R, this code will do the work for you. #Dependency library(rentrez) #Loop over your gene symbols, fetch the protein sequence and put it into a fasta file save_AAfasta <- function(IDs, nameFile) { for(i in seq(length(IDs))) { myterm ...
written 10 days ago by josev.die10
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Answer: A: Unable to retrieve Fasta of certain NCBI entries given their accession number
... You can also use the following function written in R save_AAfasta <- function(xpsIds, nameFile) { for(i in seq(length(xpsIds))) { protein <- rentrez::entrez_summary(db = "protein", id = xpsIds[i]) protein_fasta <- rentrez::entrez_fetch(db="protein", id=protein$u ...
written 10 days ago by josev.die10
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Answer: A: Loading a genome in BSgenome
... Same question here. Please, let us know if you figure out how to do it. ...
written 18 months ago by josev.die10
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Answer: A: Forge a BSgenome data package
... Your answer is exactly right. It is caused because I did not follow exactly the vignette (latest updated). There is no 'species' field for the description file. Concerning the incomplete line, I rebuilt the file and it worked. You likely have truncated your file in such a way that the final line is ...
written 21 months ago by josev.die10
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Forge a BSgenome data package
... We work on the legume Chickpea which genome has been recently released but it does not have a BSgenome package so far. I though I'd try and make one. Following the vignette I have placed some FASTA chromosomes in a folder. I have started with a small example, so I have used just the first two chro ...
bsgenome seed file written 2.2 years ago by josev.die10

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