I have single-end fastq.gz files. 

when I run RSEM with `--gzipped-read-file` it says invalid number of cammands and when i dont use it, it says `FATAL ERROR, exiting. What should I do?

    rsem-calculate-expression --star -star-path /share/pkg/star/2.5.3a -p 4 EH_25_data/EH025x045_L001/L001_R1_001.fastq.gz src_eh/rsem-ref/ref ./EH_25
Use --star-gzipped-read-file instead of --gzipped-read-file !