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  • Running kmergenie

    Hello every one.
    I'm new on bioinformatics. So, sorry if my question is too basic.
    I'm trying to run kmergenie. It hasn't worked when I use reads_file.txt with the files I want to calculate the best k-mer. That's what I'm trying:
    $ nano reads_file.txt
    -> Paste:

    ../47G_mapped_1_val_1.fq
    ../47G_mapped_2_val_2.fq


    $ kmergenie -l 21 -k 51 -s 5 reads_file.txt -o 47G_kmergenie

    The message is:
    running histogram estimation
    File reads_file.txt starts with character ".", hence is interpreted as a list of file names
    Reading 2 read files

    End then it stops.
    The only way kmergenie has worked is running one file at the time, but as I have paired end reads it's gonna take too long to finish the work.
    Please can anybody help me?

  • #2
    I think the file with the path for your FASTQs go after `kmergenie `

    Here is the program syntax: kmergenie <read_file> [options]

    I wrote this tutorial on how to use it - https://onestopdataanalysis.com/esti...-for-assembly/
    Last edited by one_stop; 03-07-2020, 09:58 PM.
    Data Scientist and blogger (http://onestopdataanalysis.com)

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    • #3
      The computer analysis of APOL1 and single nucleotide polymorphisms in chronic kidney disease (CDK). Any help anyone can provide me with will be really appreciated. Thank you very much, everyone

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      • #4
        KmerGenie estimates the high-quality k-mer period for genome de novo assembly." More info are at KmerGenie

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