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  • Vahidjj2005
    Junior Member
    • Jun 2017
    • 1
    #1

    Question: (ERR): bowtie2-align exited with value 1

    Hi I have a problem when run tophat. I have recieved this massage:
    Error running bowtie:
    Warning: output file '-' was specified without -s. This will not work in future Bowtie 2 versions. Please us -s instead.
    Warning: could not open read file "/1AM21/tophat1/tmp/index" for reading; skipping...
    Error: no input read files were valid.
    (ERR): bowtie2-align exited with value 1
    Please help me!!!

    Also, the attached link is the picture of my commend!
    Untitled hosted at ImgBB
    https://ibb.co/msadyk
    Image Untitled hosted on ImgBB
    Tags: problems, rna-seq analysis, sowftware error
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