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6 votes
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How to convert fastq to fast5

NOTICE: I have altered my answer slightly from the original as I have turned the original script into a pip installable program (with tests) and have updated the ...
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3 votes

How to convert fastq to fast5

I do this very frequently, using the read file name to identify FAST5 files associated with particular reads. If a FASTQ record includes the channel number and read number (and preferably the runID as ...
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3 votes

How to get Nanopore MinION fast5 from SRA

When I was trying to upload MinION data to SRA, they wouldn't allow me to upload only the raw signal data (i.e. FAST5 files). Every file needed to contain a FASTQ sequence, and this sequence was ...
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2 votes

How to get Nanopore MinION fast5 from SRA

I would suggest trying an alternative way, as the FAST5 is a fairly new entry in SRA - 6 public datasets as of today. You can search the ERX/ERR entry you got from SRA in ENA and either (1) direct ...
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2 votes

Understanding fast5 format

FAST5 is a proprietary format developed by Oxford Nanopore Technologies, and there's not much great documentation online. All FAST5 files will have the Raw/ field, ...
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  • 282
2 votes

How do you map nanopore fast5 files?

Fast5 files need to be converted to fastq first prior to mapping. There are currently no tools available to map the entire raw signal directly to a reference, although a few tools are available for ...
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1 vote

Understanding fast5 format

I'll give a different perspective. Oxford Nanopore FAST5 is NGS within a HDF5 database. A clear description is here. HDF5 is a format used for rapid I/O of large ...
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1 vote
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Oxford nanopore promethion; does guppy3 separate fast5 into pass and fail? If not what does?

Only if they've enabled the --qscore_filtering flag when using Guppy; this flag isn't enabled by default when running Guppy from the command line. It's a good idea ...
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