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Samtools BAM 2 Fastq conversion lose read-pair information #857

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jfy133 opened this issue Mar 22, 2022 · 0 comments
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Samtools BAM 2 Fastq conversion lose read-pair information #857

jfy133 opened this issue Mar 22, 2022 · 0 comments
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jfy133 commented Mar 22, 2022

During samtools filtering to get unmapped reads. For some reason we have the -n flag which strips the read pair information, whihc makes it difficult to convert back to pairs for e.g. de novo assembly of unmapped reads by nf-core/mag. Should remove the -n flag.
@jfy133 jfy133 added the bug Something isn't working label Mar 22, 2022
@jfy133 jfy133 self-assigned this Mar 22, 2022
@jfy133 jfy133 mentioned this issue Mar 23, 2022
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@jfy133 jfy133 closed this as completed Mar 23, 2022
@jfy133 jfy133 mentioned this issue Mar 24, 2022
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