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keep unmapped reads #15

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karlkashofer opened this issue Apr 3, 2022 · 1 comment
Open

keep unmapped reads #15

karlkashofer opened this issue Apr 3, 2022 · 1 comment

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@karlkashofer
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karlkashofer commented Apr 3, 2022 •
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Is it somehow possible to keep the unmapped reads in the output file, or at least write out the unmapped reads to a separate file instead of discarding them ?
@Daniel-Liu-c0deb0t
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Daniel-Liu-c0deb0t commented Apr 4, 2022 •
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Not at the moment. You can work around this by filtering out unmapped reads from your file before deduplication with samtools like here.

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@Daniel-Liu-c0deb0t @karlkashofer