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  • Dros
    Junior Member
    • Jun 2017
    • 1

    #1

    HISAT2 executable

    Hi

    I am trying to use HISAT2 (https://ccb.jhu.edu/software/hisat2/index.shtml) to do alignments and downstram processing.
    The problem that I encounter is that I am not able to get a hisat executable file after running the
    Code:
    make
    command (I am on Ubuntu 16.04).
    Running
    Code:
    make
    on the downloaded binary (or the source) file gives me all the other required executables (hisat2-align-s, hisat2-align-l, hisat2-build, hisat2-build-s, hisat2-build-l, hisat2-inspect, hisat2-inspect-s and hisat2-inspect-l) but not hisat2 which is required in the alignment step.
    May be I am just missing some small point here but any help will be great.

    Thanks.
    Dros
  • mastal
    Senior Member
    • Mar 2009
    • 666

    #2
    You don't need to run 'make' if you download the binary, only if you are trying to build from the source code.

    What version of HISAT2 are you using?

    I just downloaded the Linux binary for version 2.0.5, unzipped the file, and hisat2 is present, along with the other hisat2 programs.
    Last edited by mastal; 06-03-2017, 10:56 AM.

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