This repository contains the code and final data (transcript count data) for the manuscript tiled "The transcriptomic effects of acute UV radiation exposure on two Syntrichia mosses" published in X.
The script clean_rna.sh uses Trimmomatic vs. 0.30 to quality rim raw reads
The script tophat_paired-end_acute.sh assembles the read to the S. caninervis genome/transcriptome
The scripts htseq-count_acute-BR.sh and htseq-count_acute-SC.sh estimate transcript counts for each genome for S. caninervis (SC) and S. ruralis (BR)
Using the count data in R, the script timeseries.R performs differential abundance/expression analyses and produces summary tables and plots
Finally, the R script test_OGs_DPs_ELIPs_LEAs.R counts ELIPs and LEAs in the summary tables from the differential abundance analyses.