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  • Trimming Fastq Reads for kallisto

    Does kallisto match reads that are below that of the K-mer length used to
    create the index? For example, the default K-mer value for creating the index
    for kallisto is N=31. If I set trimmomatic MINLEN=20 and I get some reads
    trimmed to < 31 bases, are these tested against the hash of 31 bases within
    the index and not found (inefficient, tested but not counted), ignored because
    they are too small for the K-mer length (inefficient, tested for length and
    ignored), or matched as a substring of the K-mer within the index and counted
    (flexible, some amount of mismatch allowed)?
    --
    Paul N. Hengen, PhD
    http://www.linkedin.com/in/hengen

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