Tutorial_GenomeEvolution
Genome Evolution Lecture for Phylogenomics Workshop
Framework for learning some basic Evolutionary Genomics and Comprative steps
Requirements:
- R
- R packages “ggplot2”,”gridExtra”,”dplyr”,”RColorBrewer”, "pheatmap"
- R/Bioconductor packages AnnotationDbi and tximport
- install these packages with
Rscript scripts/install_pkg.R
Data
-
there are data in the data folder and you should run download.sh for an example of how to download data from FungiDB data/dna_species.dat lists the names of the species to download. These are the prefixes for the files in this folder at FungiDB http://fungidb.org/common/downloads/Current_Release/ - note you want the name of folders which list the strain eg Umaydis521 not Umaydis which is where the genome data are located.
-
pre-run OrthoFinder results are in analysis/ortho_set1/Results see the Orthogroups.csv and Orthogroups.GeneCount.csv for orthologs contain See the Orthogroups_UnassignedGenes.csv for genes which are not in a cluster
scripts
- plot_chroms_1.R is an R script to generate some summary graphics from GFF files
- plot_heatmap_family.R is an R script to generate a heat map for gene family sizes
- extract_orthologs_single-copy_Afum.py is a python script to
Run the R script Rscript scripts/plot_chroms_1.R
- see the output in plots Rscript scripts/plot_heatmap_family.R
- see output in plots - also walk through each line one at a time in Rstudio or elsewhere
run the pythonscript to see how to extract gene families which are single-copy for the two Afumigatus strains ./scripts/extract_orthologs_single-copy_Afum.py