I am using rsem to calculate expression levels in a dataset of paired end reads. I want to use STAR as the aligner. I have written the command like this:
rsem-calculate-expression --star -p 16 --paired-end DT_01_R1.fastq DT_01_R2.fastq /path/to/reference/genome/ rsem_output/DT_01
I'm pretty sure this will work, What I don't know is this: do I need to generate an annotated reference genome for STAR before running this? I'm using the zebrafish genome, and I have downloaded both the .fasta file and the .gtf file from Ensembl. What do I need to do with these before I run the aligning and expression calculation I've written above? Or do I just point it to the directory containing the .fasta and .gtf files? Thanks very much!