16 May 2014

ddRADseq, LaTex, Silene, git, and rmarkdown

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May 12 - 16 notes



Finished plotting when expression increases or decreases. Significant differences between colonies, but is it biologically meaningful?


SHC ran PCR on samples with varying amounts of adapters from ligation step. Worked! Looks like adapter concentration was too low in ligation step and required empirical determination.


Eckert, A.J., Bower, A.D., Wegrzyn, J.L., Pande, B., Jermstad, K.D., Krutovsky, K.V., Clair, J.B.S. & Neale, D.B. (2009). Association Genetics of Coastal Douglas Fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-Hardiness Related Traits. Genetics, 182, 1289–1302.

Eckert, A.J., Wegrzyn, J.L., Liechty, J.D., Lee, J.M., Cumbie, W.P., Davis, J.M., Goldfarb, B., Loopstra, C.A., Palle, S.R., Quesada, T., Langley, C.H. & Neale, D.B. (2013). The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae). Genetics, 195, 1353–1372.

Walsh, B. & Blows, M.W. (2009). Abundant Genetic Variation + Strong Selection = Multivariate Genetic Constraints: A Geometric View of Adaptation. Annual Review of Ecology, Evolution, and Systematics, 40, 41–59.

Yin, T., Cook, D. & Lawrence, M. (2012). ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biology, 13, R77.



Finished tech report - sent to Steve





Changed manuscript document to be compatible with the rmarkdown package. Added YAML header:

and can now compile PDF with citations directly from RStudio! In theory, can also do from command-line using Rscript -e "library(knitr); library(rmarkdown); render('input.Rmd')" though I haven’t tested this.


Analysis. Writing. Getting there!!!

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