The dataset that I am working with comes from a producer cell line that expresses a recombinant protein. Therefore, I was wondering how I could modify the reference .fasta and .gtf files in order to include the sequence of the recombinant molecule. Are there any convenient functions/packages for that job in either python/R/terminal? Is there anything that I need to be careful about? A potential candidate that I have found is reform1; does anyone have experience with this package?