Upload data directly into a collection! Solves: No compatible list of pairs dataset collections available

2

Welcome @turbine

I’ll try to explain the tool from and how to get the dataset selected!

You have paired end data, correct? Two files, one for the forward reads and one for the reverse reads?

The tool is scanning for a collection shape in your active history.

If you have multiple tabs open in your browser, you might just need to reload your browser to make sure that the active history is correct, so start there!

Then, the tool is looking for a particular shape for the data and that the input data has an accepted datatype format. This makes sure that the parameters on the tool form are correct for your particular data.

How to make a collection → Why collections?

Example for selecting a paired collection for SPAdes

spades-paired-end-input-1
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There are two types of fastq data shapes for the paired end input:

  • interlaced reads: both forward and reverse reads in the same fastq dataset
    • single or multiple datasets with interlaced fastq reads
    • a list collection with one interlaced fastq dataset per sample
  • separate reads: one fastq dataset for forward reads, one for the reverse reads
    • a paired list collection organized by sample, with each containing two datasets

There are several types of fastq data formats:

  • these are the same for any of the selections
  • getting the datatype format is especially import for fastq data since this is metadata that is describing how the quality scores are scaled!
  • loading data with all default settings in the Upload tool is one way to ensure that this is correct! → Getting Data into Galaxy
  • You can also click on the pencil icon for a dataset and redetect the datatype. → FAQ: Detecting the datatype (file format)
  • Tools like FastQC and Fastq info can also help if you need to investigate the format more

This screenshot shows a paired end list collection in the history, and the settings on the tool form that will select it.

spades-paired-end-input-2
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This is that history shared if you want to see how it works.

I’m guessing that you have two files – one for the forward and one for the reverse – but these are not in a collection yet? We have lots of help!