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6

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 links and code snippets accordingly. The essence of the answer is still exactly the same. This is something I have been meaning to get around to for a while, so thanks for the prompt. I have ...


3

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 well), then I use that information to find the associated FAST5 read. If reads are called with Albacore, then the sequencing_summary.txt file has additional ...


3

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 extracted from the file and stored in the archive. Given this, I don't expect it will be possible to retrieve signal or event information from SRA. I also don't ...


2

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 download it via ftp or (2) redirect to Galaxy. Here's a tutorial that might be interesting for you: basically, you first get the archive from ENA, then find ...


2

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 identifying short sequences within the raw signal.


1

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 to use all fast5 reads for recalling, because accuracy improves over time, so some that previously failed may slide into the pass folder. FYI, I'd be much happier if people asked their nanopore ...


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