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  • In need of help with gsAssembly

    To all,
    I am trying to use the gsAssembly package to sort my .fna file into MIDs. I had to add MIDs to the MIDconfig.parse file. I am running the assembly GUI with cDNAs, and multiplexed option. When I select the MIDconfig.parse file and then set my parameters, such as contig and provide consensus etc., It seems to be working but then when I check results, it shows a warning on every MID--- "waning: nonzero exit value for MID1" I have tried to read the manual, however, I don't know how to use the sfffile or the -mcf option. Do I do this in the terminal or in the GUI? and also, exactly how do I do this to get the program to use my MID file? Please in need of immediate help !!!!!

    clackbeatr

  • #2
    In a terminal, try
    Code:
    sfffile -s yourfile.sff
    or
    Code:
    sfffile -mcf yourmidfile.txt -s yourfile.sff
    If you don't get your sff file split into one for each MID, there may be something wrong with the MIDfile.

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