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Check if flowcell id is uniform in a fastq file #1716

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pmoris opened this issue Oct 30, 2024 · 0 comments
Open

Check if flowcell id is uniform in a fastq file #1716

pmoris opened this issue Oct 30, 2024 · 0 comments
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enhancement New feature or request

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@pmoris
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pmoris commented Oct 30, 2024

Description of feature

This is an extension of #1664

The proposal above adds a check to determine whether the first read of a paired fastq sample shares its flowcell id. However, if a user were to supply a fastq file that was merged from different fastq files of the same sample (e.g., across lanes or sequence runs), the flowcell id would not be the same for all reads in the fastq file.

Ideally we'd add a check to ensure that this is the case (seqkit?), or if possible, use something like fastp to split the files into separte fastq files with uniform flowcell ids?

@pmoris pmoris added the enhancement New feature or request label Oct 30, 2024
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