User: Simon Coetzee

gravatar for Simon Coetzee
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50
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New User
Location:
USA Cedars-Sinai Medical Center
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3 years, 11 months ago
Joined:
7 years, 9 months ago
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s*******@gmail.com

Posts by Simon Coetzee

<prev • 7 results • page 1 of 1 • next >
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Answer: A: motifbreakR VariantAnnotation namespace error on reading vcf file
... Yes, there was a problem in the snps.from.file function. Thanks for the extra eyes. Fixed it up, it should be in the next build of the package, 1.0.1, tomorrow. Or you can get it from github now. ...
written 4.0 years ago by Simon Coetzee50
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readVCF with 1000 genomes data from 20130502 fails to return genotype information
... When running readVCF with 1000 genomes data from 20130502 no genotype is returned. I believe this to be because readVCF looks for a description of the FORMAT field in the header of the vcf file, but in the latest version of 1000 genomes, this is not present. It seems based upon my reading of the sp ...
vcf readvcf tabix written 4.3 years ago by Simon Coetzee50 • updated 4.3 years ago by Valerie Obenchain6.7k
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BiocUpgrade without being promped to confirm
... How would one go about automating updating to the newest bioconductor install.  I have many machines that I have to update to 3.0, and the command: biocLite("BiocUpgrade", ask=FALSE) still requires intervention with the following: Upgrade all packages to Bioconductor version 3.0? [y/n]: Is the ...
biocinstaller bioclite biocupgrade written 4.9 years ago by Simon Coetzee50 • updated 4.9 years ago by Dan Tenenbaum8.2k
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Rsubread for paired end SOLID sequencing
... Hi Wei, I have one more question. (I hope its just one more). Is there a way to have subread use a qual file in addtion to a csfasta file, or would I need to convert to some kind of csfastq? Simon On Mon, Jul 29, 2013 at 8:44 PM, Wei Shi wrote: > Hi Simon, > > I have just added 'col ...
sequencing alignment convert rsubread written 6.1 years ago by Simon Coetzee50 • updated 6.1 years ago by Wei Shi3.2k
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Comment: C: Rsubread for paired end SOLID sequencing
... Thanks for the help, everything is running smoothly now. Only one more question, is there an option in Rsubread equivalent to "-b" in Subread (to output the sam file in basespace format, when starting from colorspace fasta)? Thanks again, Simon Coetzee Centro Regional de Hemoterapia Hospital das ...
written 6.2 years ago by Simon Coetzee50
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Rsubread for paired end SOLID sequencing
... I have some paired end SOLID sequencing data, the protocol using F3/F5 fragments (not the simpler F3/R3). Both fragments come from the same strand. Some of the nuances are explained here: http://www.biostars.org/p/48597/ Having read the manual for Rsubread, its clear that it can handle SOLID sequ ...
sequencing rsubread written 6.2 years ago by Simon Coetzee50 • updated 6.2 years ago by Wei Shi3.2k
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GenomicRanges functions unlist(GRangesList(x)) throw an error when used from an installed package
... When I install a package of my own creation that uses the GenomicRanges package,?I get an error: Error in unlist(x) : argument not a list the example function that throws this error is: TestFunction <- function (z) { ? ? x <- GRangesList(z) ? ? y <- unlist(x) ? ? return(list(x, y)) } I ...
written 7.8 years ago by Simon Coetzee50 • updated 7.8 years ago by Vincent J. Carey, Jr.6.3k

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Popular Question 4.0 years ago, created a question with more than 1,000 views. For BiocUpgrade without being promped to confirm

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