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  • 2
    What is your question exactly? Commented May 30, 2019 at 22:44
  • 1
    What do you mean by "longer codes"? Commented May 30, 2019 at 22:44
  • I was hoping I could apply this to mapping multiple fastq files and naming the output. Commented May 30, 2019 at 22:45
  • Something Like this: while IFS=" " read -r f1 f2 f3; do rsem-calculate-expression --star --star-path /share/pkg/star/2.7.0e/bin --temporary-folder --star-gzipped-read-file --paired-end $f1 $f2 ../genome_indices/rsem-star/rsem-star --outFileNamePrefix $f3; done < ../src_pdm3012/input.sample.text But it does not work Commented May 30, 2019 at 22:46
  • 3
    How does it "not work"? What are the error messages? I'd suggest editing your question and putting this very relevant information in it. Commented May 30, 2019 at 22:49