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  • HTSeq problem on Windows

    Hi, I would appreciate any hints anyone might have on this one.

    I am trying to get HTSeq-count to work on my Windows 7 machine in order to prepare data for DESeq. Installation went fine, but whenever I try to run it, it processes all the lines in my GFF file and then a pop-up window comes up saying "python.exe has stopped working. A problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available"

    Right before this pops up, it says "Warning: Malformed SAM line: RNAME != '*' although flag bit &0x004 set". But in my searches on this forum, people seem to say this warning can usually be ignored, so I'm not sure it's related to my problem, besides indicating that HTSeq has gotten to the step of processing the SAM file before causing the problem.

    I've tried this on a couple different SAM files form different sources (that were name-sorted as BAM files and then converted to SAM using SAMtools) and the same error always pops up. My GTF file is the human file from Ensembl. Any ideas? Is this most likely a problem with HTSeq, my installation, or even my machine? I don't know where to look.

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