I work mostly within the R and python programming environments. Here, I have uploaded some code snippets that other people may find useful. If you would like to use these scripts but are having trouble implementing them, feel free to contact me and I may be able to help.
This small function parses the output of Structure for plotting in R with the function barplot(). I have not tried it on other data sets other than my own, so there’s a good chance you may run into errors.
This short python script takes a Trinity assembly as input, extracts the longest isoform for each contig, and outputs a new assembly with only the longest isoform for each Trinity component.
If you find the compselector script useful, please cite the following paper, which is what I developed the script for, and also provide a direct link to the compselector code:
Mason, N. A., & Taylor, S. A. (2015). Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird. Molecular Ecology, n/a–n/a. doi:10.1111/mec.13140.