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Understanding min_kmer_matches in fastqtools.filter_by_sequence #54

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paulbrodersen opened this issue Nov 21, 2019 · 0 comments
Open

Understanding min_kmer_matches in fastqtools.filter_by_sequence #54

paulbrodersen opened this issue Nov 21, 2019 · 0 comments

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@paulbrodersen
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paulbrodersen commented Nov 21, 2019 •
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I am trying to understand the default value for min_kmer_matches in fastqtools.py : filter_by_sequence. The default value for min_kmer_matches is 20 whereas the default kmer_size is 10. As far as I follow the code, the maximum number of bases that can match the k-mer can hence also only be 10. Am I missing something, or do the defaults need adjustment? I would appreciate a second opinion. The relevant file is here.
@paulbrodersen paulbrodersen changed the title min_kmer_matches in fastqtools.filter_by_sequence Understanding min_kmer_matches in fastqtools.filter_by_sequence Nov 21, 2019
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