What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with matching fast5?
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17 months ago
O.rka ▴ 390

I want to run nanopolish and I have some large fastq files. I want to subsample them but I also need the fast5 for the subsampled reads. What is the best method to do this considering the size distributions of the ONT reads?

sequencing • 701 views
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Hi O.rka, did you manage to find the best way to downsample your dataset?

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28 days ago
O.rka ▴ 390

I didn’t end up doing it but check out this thread. There is a tool that is recommended: https://github.com/nanoporetech/ont_fast5_api/issues/36

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