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  • Tuxedo suit

    Hello!

    I am rying to run tophat it doesnt seem to work.
    i have loaded the modules and everything(i think) nothing!
    i think its something wrong with my script!
    Please help


    bowtie2-build Arabidopsis_thaliana.fa Arabidopsis_thaliana

    tophat2 p 5 -library-type fr-firststrand -o Control1_tophat_output Arabidopsis_thaliana Control1_trimmed.fq
    tophat2 p 5 -library-type fr-firststrand -o Control2_tophat_output Arabidopsis_thaliana Control2_trimmed.fq
    tophat2 p 5 -library-type fr-firststrand -o Control3_tophat_output Arabidopsis_thaliana Control3_trimmed.fq
    tophat2 p 5 -library-type fr-firststrand -o Case1_tophat_output Arabidopsis_thaliana Case1_trimmed.fq
    tophat2 p 5 -library-type fr-firststrand -o Case2_tophat_output Arabidopsis_thaliana Case2_trimmed.fq
    tophat2 p 5 -library-type fr-firststrand -o Case3_tophat_output Arabidopsis_thaliana Case3_trimmed.fq
    Last edited by Nathan Seth; 06-01-2017, 02:01 PM.

  • #2
    Maybe try "-p 5" instead of "p 5"?

    Comment


    • #3
      That's probably it. Also, it's very helpful to show the error message you get.

      Comment


      • #4
        In addition to previous suggestions, some options require two hyphens (e.g. --library-type fr-firststrand).

        Comment

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