User: Simon Coetzee
Simon Coetzee • 50
- Reputation:
- 50
- Status:
- New User
- Location:
- USA Cedars-Sinai Medical Center
- Last seen:
- 3 years, 11 months ago
- Joined:
- 7 years, 9 months ago
- Email:
- s*******@gmail.com
Posts by Simon Coetzee
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... 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 Coetzee • 50
2
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1
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712
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... 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 ...
written 4.3 years ago by
Simon Coetzee • 50
• updated
4.3 years ago by
Valerie Obenchain • 6.7k
6
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... 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 ...
written 4.9 years ago by
Simon Coetzee • 50
• updated
4.9 years ago by
Dan Tenenbaum • 8.2k
1
vote
1
answer
715
views
1
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... 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 ...
written 6.1 years ago by
Simon Coetzee • 50
• updated
6.1 years ago by
Wei Shi • 3.2k
0
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716
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... 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 Coetzee • 50
0
votes
1
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716
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1
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... 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 ...
written 6.2 years ago by
Simon Coetzee • 50
• updated
6.2 years ago by
Wei Shi • 3.2k
0
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1
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1.4k
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1
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... 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 Coetzee • 50
• updated
7.8 years ago by
Vincent J. Carey, Jr. ♦ 6.3k
Latest awards to Simon Coetzee
Popular Question
4.0 years ago,
created a question with more than 1,000 views.
For GenomicRanges functions unlist(GRangesList(x)) throw an error when used from an installed package
Popular Question
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