Hi, I have an existing dataset from nanopore run in fast5 format. I’m using GALAXY to convert it into fastq format. The tools which I’ve trialled from the tools list are : 1) extract fastq in tabular format from a set of fast5 files and 2) extract read in fasta or fastq format from nanopore files. …

Hi @jas This error indicates that a tar archive was loaded and used for the input. For many cases when a tar archive is uploaded, only the first file in the archive is loaded. That first file can be an index, which won’t contain any reads. These tools are working at UseGalaxy.org using the tool’s …

Hi there, Good day to you. Thank you for your reply. I’ve had a trial on nanopore tar upload test, I can’t seem to get it detect my dataset named: simulationdataset.fast5 I’m working on usegalaxy.org (e.g. Galaxy | Accessible History | nanopore tar upload test ). For the galaxy version, i run the…

hi @jas Data in h5 format with that datatype assigned should work fine with these tools. I’m going to send you a direct message with how to share your history privately so we can review it and provide better feedback. We won’t post anything private back to the public topic but may summarize genera…

Update: The dataset had some content (and perhaps format) issues. Those are being worked out. No details or workarounds to share with the community at this time should anyone else run into the same type of odd results/errors from these nanopore parsing tools (yet).

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Nanopore data upload, format/datatype, and unexpected results from tools

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