The pipeline needs the data "cleaned_07082022.rda" as a start.
I created 3 Rmd files to prep the 3 different RE.
You should run first "01.LTR_retrotransposons.Rmd" as the grooming step is done in this file only.
Then you can run "02.L1_retrotransposons.Rmd" and "03.Alu_retrotransposons.Rmd".
Within each file, I ran the prediction, trimming and aggregation steps. After each of the step, I saved a rds file for a faster run of the file.
You will have to un-comment the code to create the rds the first time.