Hi all,

My RNA libraries are constructed from U2OS cell lines with plasmids containing genes of interest. I'm particularly interested to see whether there are any mutations within the plasmids, so besides mapping my libraries onto hg38 genome, I also provide all the plasmids I put in the cell lines in the parameter --genomeFastaFiles. My question is: Do I need to provide the gtf file for these plasmid fasta files and do I need to create indices for them? In my BAM file, I can see that my reads are mapped to the plasmids, but I'm not sure whether that is sufficient or not. Thank you in advance for everyone's help and suggestions