27 March 2013

aphaenogaster, pandoc, transcriptomics, and simulations

Next post Previous post



Continuing working on permits for Aphaenogaster collection.


Planning to simulate sequence data to develop and evaluate transcriptome assembly pipeline, follow method of Vijay et al (2013)

  • Vijay, N., Poelstra, J. W., Künstner, A., & Wolf, J. B. W. (2013). Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments. Molecular Ecology, 22(3), 620–634. doi:10.1111/mec.12014
  • Moreau, C. S., & Bell, C. D. (2013). Testing the Museum Versus Cradle Tropical Biological Diversity Hypothesis: Phylogeny, Diversification, and Ancestral Biogeographic Range Evolution of the Ants. Evolution, n/a–n/a. doi:10.1111/evo.12105

Lab notebook

Test of showing R code in lab notebook

x <- seq(1:10)
y <- x^2

To actually run this R code and generate results, simply run through knitr

When converting pandoc to pdf, the default latex settings gave HUGE margins. stackoverflow gave the answer:

pandoc -V geometry:margin=1in -o output.pdf input.md


  • Ormeño-Orrillo, E., Servín-Garcidueñas, L. E., Imperial, J., Rey, L., Ruiz-Argueso, T., & Martinez-Romero, E. (n.d.). Phylogenetic evidence of the transfer of nodZ and nolL genes from Bradyrhizobium to other rhizobia. Molecular Phylogenetics and Evolution. doi:10.1016/j.ympev.2013.03.003

  • Gelman, A. (2013). P Values and Statistical Practice. Epidemiology, 24(1), 69–72. doi:10.1097/EDE.0b013e31827886f7

Creative Commons Licence
This work is licensed under a Creative Commons Attribution 4.0 International License.