User: e.rempel
e.rempel • 790
- Reputation:
- 790
- Status:
- Trusted
- Location:
- Germany, Heidelberg, COS
- Last seen:
- 3 months, 3 weeks ago
- Joined:
- 4 years, 9 months ago
- Email:
- e*******@dkfz-heidelberg.de
Statistician/bioinformatician.
Posts by e.rempel
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... Hi,
I have a question regarding the output of the tool *varscan pileup2snp*. The input is the pileup file generated by *samtools mpileup* without reference. One particular line from the input is
1 16259813 N 80 G$g$aaGAGAaggaAGGaaGaGAgaAGaAgAAGGaAAAAAGAAaaGAaGgGgAGaGAGAgGggGAAAAgAAGgggAGGGAA^] ...
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... Hi everyone,
I have a question regarding the usage of **bcl2fastq** for an Agilent panel. The manufacture suggests [in this guide][1] to use the parameter "---use-bases-mask" with the specification Y\*,I8,Y10,Y\*.
Bcl2fastq throws in this case the error:
UseBasesMask formatting e ...
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Comment:
C: aligning with STAR
... After depreciation of homebrew/science you have to use
brew tab brewsci/science
brew install rna-star ...
written 20 months ago by
e.rempel • 790
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... Hi,
in the example from [Bioconductor][1] the object after **cutree** execution contains the genes with the cluster identifier (a number from one to n - an integer you have chosen for cutree).
[1]: https://support.bioconductor.org/p/93424/ ...
written 22 months ago by
e.rempel • 790
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... Hi,
as you said, the p-value of Fisher's exact test is highly significant. The reason for this, as you have also said, is the size of gene's universe.
I have seen some people making thoughts about the universe: can any random gene from these 17611 genes be selected in any of your lists? Sometimes ...
written 22 months ago by
e.rempel • 790
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... Please, consider upvoting ("thumbs up") or accepting the answer, if it clarifies the issue for you. ...
written 23 months ago by
e.rempel • 790
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... I am not a huge expert on cummeRbund, but it looks like you first extract the genes from `cuff` object, then you use them to create MDS-plot. Usually, the input for MDS (or PCA) is some rectangular data, e.g. genes in rows, samples in columns. For me it looks like you are using just "genes". Am I ri ...
written 23 months ago by
e.rempel • 790
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... Just hook your boss up on [biostars][1] ;)
[1]: http://biostars.org ...
written 23 months ago by
e.rempel • 790
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... So, what should colour represent? I honestly don't get it. ...
written 23 months ago by
e.rempel • 790
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Answer:
A: try command in R
... Hi,
quick Google search redirected me to the [book][1] of Hadley Wickham. Here he suggests:
> To pass larger blocks of code to try(), wrap them in {}:
try({
a <- 1
b <- "x"
a + b
})
HTH
[1]: http://adv-r.had.co.nz/ ...
written 23 months ago by
e.rempel • 790
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