read simulation and quantification

Question

[snishtala03]

Hello,

I have fasta sequences of 7 viral RNA transcripts. I need to see if I can recover the correct counts of these transcripts.

I am guessing I will first have to use a software ( like polyester or rsem) to generate simulated fastq files for these transcripts and then use a transcript assemble software (like trinity or stringTie) to quantify them.

Please suggest if this is the right way of doing it and tools I can use to get my results?

Thank you for your help!