Hello Genomax, thank you for replying. What I want to do is generate realistic RNA-seq data from the reference transcript.

I tried using polyester to generate realistic RNA-seq data from the reference transcript. It would be nice for this realistic rna-seq to be illumina profiled, introducing hexamer bias, positional bias, and SNP (indels). If there is a better tool than polyester to generate rna-seq from reference transcript, that would be great too. I am not just sure how many parameters should I include in the reference transcript to generate realistic enough rna-seq data. There is another tool like ART, but ART is a pretty old package, almost a decade ago.

I originally thought if there is realistic RNA-seq generated from reference transcript, that would be great.