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Problem using HTSeq



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  • Problem using HTSeq


    I am currently using HTSeq to get raw counts. HTSeq has been installed on our linux cluster and the administrators suggested to use export PATH=... in order to use it. However, I am getting following error:

    Traceback (most recent call last):
    File "/opt/HTSeq/bin/htseq-count", line 3, in ?
    import HTSeq.scripts.count
    ImportError: No module named HTSeq.scripts.count

    I am not able to figure out the reason. Anyone of you faced the same problem and found solution?

    Please share your suggestions.

    Thank you,


  • #2
    I have the same issue! Could someone help with this?
    Did you figure it out already pinky?


    • #3
      HTSeq has been installed incorrectly. The PATH setting allows your shell to find the htseq-count script in its non-standard location in /opt/HTSeq/bin/, but this script is just a three-line file that tell Python to load HTSeq and the 'count' submodule. As HTSeq has not been installed into the standard Python package path, you also have to set the PYTHONPATH variable. I believe that the distutils install function that I used displays a warning about this whenever it is asked to install to a non-standard location.

      It might be easier if you installed HTSeq yourself with 'python setup.py install --user', as suggested in the installation instructions.


      • #4
        Hi Simon,

        I have the same problem as pinky, I installed setuptools and then installed HTSeq using 'python setup.py install --user' as suggested. Still, htseq-count is not added to my path. I did "import HTSeq" on a python shell and I get no errors. Do you have any suggestions? I'm running python 2.7.3.


        • #5
          Issue solved, the script was added to ./local/bin instead of /bin. Thanks.