In this project we are using RNA-seq to understand gene expression during different phases of Phytophthora cinnamomi (Pc) infection of Lupinus angustifolius (La).
Here is the contents of the repo:
idx.sh is the script used to index the reference genome which is the combination of Pc and La genomes and annotations
run_star.sh is the script used to map reads to the ref genome.
samplesheet.tsv is the list of samples and labels for statistical analysis
stats.Rmd is the Rmarkdown file used for statistical analysis of the data.