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multiqc and Kraken (with unclassified reads) #126

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thomasmanke opened this issue Nov 8, 2023 · 0 comments
Open

multiqc and Kraken (with unclassified reads) #126

thomasmanke opened this issue Nov 8, 2023 · 0 comments

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@thomasmanke
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If kraken*report contains samples with a line containing "unclassfied" reads and other samples containing no such line then multiqc will interpret the former as "kraken" and the latter as "bracken" output - this will result in two different sections and also screw the parsing of the multiqc_report.json

An example is here: 20230607_0958_P2-7085206e51685c-B_PAO92085_9bf914e7

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