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Error: duplicates in sam-header when running Bowtie2 on full NT #122

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LeandroRitter opened this issue Mar 2, 2023 · 2 comments
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Error: duplicates in sam-header when running Bowtie2 on full NT #122

LeandroRitter opened this issue Mar 2, 2023 · 2 comments

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@LeandroRitter
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When following up KrakenUniq hits with Bowtie2 on full NT and not on the PathoGenome (default), there is an error originating from duplicate records in the sam-header. One needs to grep the duplicates, clean the header, and replace it in the sam-file. I have the codes that do it, and will push a commit that fixes this issue soon.
@LeandroRitter LeandroRitter mentioned this issue Mar 2, 2023
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@percyfal
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percyfal commented Mar 3, 2023

Re PR #123 ; now I see what you were doing, should have read this first!

@LeandroRitter
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fixed with new commit #123

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@percyfal @LeandroRitter