rnaSPADES --nanopore: Confirming data format and shape for an input area

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Hello,

I am experiencing difficulties loading Nanopore reads to rnaSPADES via the “Additional read file” section.

I was able to combine Illumina reads into a dataset of paired end reads, but the ONT fastq.gz file (output from guppy basecaller) could not be loaded/recognized in the “Additional read files > Nanopore reads” box. The original FILE.fastq.gz nor a flat dataset list with this file is accepted.

How can I add the nanopore reads to rnaSPADES?

Best,

2

Hello @ARW-UBT

Hopefully we can help!

For this part

I am wondering if a small change to the dataype format assigned to the dataset will help! A more specific format can be directly assigned or detected (using the pencil icon). More details. → FAQ: FASTQ files: `fastq` vs `fastqsanger` vs ... Your ONT reads are fastqsanger and if compressed you can assign fastqsanger.gz. Or, use the re-detect option and the process will confirm the compression status while assigning that format type.

Why? SPAdes is considering the quality scores for these inputs, so the more specific datatype is a type of “appropriate data” check added in. The screenshot below is of the tool form with the accepted formats sections toggled open. I included the transcript input option as a comparison – that input can be in other formats since only the bases are considered, and quality scores, if present, would be ignored.

datatypes-rnaspades-ONT-reads
datatypes-rnaspades-ONT-reads988×862 88 KB

[1]

A dataset becomes available on a tool form when three conditions are met:

  1. The dataset is in the active history
  2. The datatype format assigned to the dataset matches one of the accepted formats listed for an input area
  3. And, the shape of the data is a match for what that input is configured to search for – these are the individual dataset, versus multiple datasets, versus list collection, versus list of pairs collection options toggled in the select menu.

You’ll learn to recognize when one of these is mixed up as you use Galaxy more! The extra baked in QA really does save us all from crazy odd errors. :slight_smile: A short reference for navigation is in this little guide with a big name! → Hands-on: Understanding Galaxy history system / Understanding Galaxy history system / Using Galaxy and Managing your Data

Please let us know if this actually solves your specific problem or not! If I guessed wrong, maybe share some screenshots and I’ll try to help more? Or you can share the history itself and let us know the ONT dataset number and I’ll see if I can reproduce to come up with a better solution. Thanks!

  1. rnaSPAdes tool form with the Additional read files section expanded, and arrows pointing to the data shape toggle and the accepted formats area (expanded). ↩︎

3

This did the trick! The job is now running.

Thanks for you support!

Best,

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