rsem-calculate-expression regarding

[amodvet]

Hi.
I am using RSEM for the first time and facing some difficulties. Firstly I ran 'rsem-prepare-reference' on paired end data and got many output files (e.g. .idx.fa, n2g.idx.fa, .chrlist, .seq etc.).

Could you please help me telling the file which would be used as reference file in 'rsem-calculate-expression' command. Though, I have used "$rsem-calculate-expression -p 8 --paired-end 4R_1.fastq 4R_2.fastq ref_file 4R_paired_end_quals" command but got an error "Could not locate a Bowtie index corresponding to basename "ref_file".
Thanks