User: e.rempel

gravatar for e.rempel
e.rempel790
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

<prev • 90 results • page 1 of 9 • next >
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Understanding the output of pileup2snp
... 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^] ...
variant samtools snp varscan written 5 months ago by e.rempel790 • updated 3 months ago by Biostar ♦♦ 20
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bcl2fastq creates only Undetermined fastq
... 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 ...
software error sequencing written 9 months ago by e.rempel790 • updated 9 months ago by genomax76k
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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.rempel790
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Comment: C: Clustering and extracting gene IDs with same expression profiles
... 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.rempel790
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Answer: A: On the significance of the overlap between lists of genes
... 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.rempel790
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Comment: C: Submission of RNA-seq data in NCBI Sequence Read Archive (SRA)
... Please, consider upvoting ("thumbs up") or accepting the answer, if it clarifies the issue for you. ...
written 23 months ago by e.rempel790
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Comment: C: Getting MDSplot from Cufflinks data [cummeRbund]
... 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.rempel790
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Comment: C: scatter plot in ggplot2 two colour for two different condition
... Just hook your boss up on [biostars][1] ;) [1]: http://biostars.org ...
written 23 months ago by e.rempel790
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Comment: C: scatter plot in ggplot2 two colour for two different condition
... So, what should colour represent? I honestly don't get it. ...
written 23 months ago by e.rempel790
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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.rempel790

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Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: GO analysis using topGO Arabidopsis
Scholar 10 months ago, created an answer that has been accepted. For A: Problem with topGO: GO term enrichment analysis
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