I want to make index files before map RNA-seq reads on STAR. then I need to use theses alignments as an output of TEToolkit analysis. so two annotation files mask repeated and genes are provided. for Indexing as TEToolkit manual mentioned In order to map RNA-seq reads, STAR needs an index file of the reference genome and transcriptome. I made an index by using primary assemble reference genome (fasta file) and repeated mask gtf file, then mapped reads on. is it correct? because I just wanted to quantify TE elements, but TEtoolkit needs another option GTF file for gene, I think its index also should be provided. would appreciate any help?