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  • neavemj
    replied
    I think you need to specify the output file. For example, add "-S new_file.sam" to the script.

    Cheers,

    Matt.

    Leave a comment:


  • Pery
    started a topic Alignment with bowtie doesn't creates .sam file

    Alignment with bowtie doesn't creates .sam file

    Hi,

    I'm trying to align a fastq.gz file with bowtie.
    My script is:
    ${bowtie_source} --sam --best ${ref_genome} ${fastq_file}

    But it doesn't carets a new .sam file.
    How to fix the script in order to get a .sam file in a desired directory?

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