Input data for nanopore analysis

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Hi everyone, i have some fastq files which are from different samples and want to analyse them first starting of using ARTIC guppy in the galaxy.eu. How do I input the files? Do I just put them in separate as ‘regular’ or as a list?

I am not sure if i have inputted correctly?

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Also, after this I want to take the data and further analyse using nanofilt which is not available in galaxy.eu. I have to take the next bit of data to galaxy.au.

Best wishes

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Welcome, @Martyn

You should organize the reads into collections as described under the input area in the note.

If you are not sure how to do that, start with these tutorials Search GTN Materials (query=collection).

You want to create a “list of lists”. One list at the top that contains nested lists, one per sample, where each contains all the reads for that particular sample.

There are a few ways to do this.

Simple. Fine for smaller amounts of data.

  1. Select all datasets for sampleA and put those into a list collection. Name the collection with the sample name.
  2. Do the same for sampleB, sampleC, … sampleN.
  3. Use the tool Build list to nest all of those collections into a top level collection.

Rule Based. Good for all use-cases but involves a bit more prep.

  1. Too much to post here, see the tutorials instead please Search GTN Materials
  2. Rule-based processing can load data by URL (find it as a tab in the Upload tool) or directly from data in the history (find it in the tool panel in the group Collection Operations).

Note: Simple names are best for collection naming. Use oneWord with no special characters.