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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

      Comment


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

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