Hi there.
I am having some issues while trying to use rnaviralspades tool. I have paired reads that I would like to analyze. First I used Trim Galore, for trimming and my output files are in fastqsanger.gz format. However, when I want to run the rnaviralspades tool, there is a warning appearing in the Single-end or paired-end short-reads parameter: “No compatible list of pairs dataset collections available”.
Would you please help me to solve this problem. Thanks a lot.
In the history, use Select Datasets on the left side of that panel, check/uncheck the datasets you want to combine, then choose Build List of Dataset Pairs on the right. A pop-up will open where you can name the folder. Then go back to the tool form and it will recognize the collection folder if the format datatype of the data inside a folder is a fit for the tool (you can also just drag it on top of the input area).
If you use default options when building the collection, the original datasets will be marked to sort into the Hidden tab of the history, simplyfing the Active tab view. You can unhide these whenever you want to, or not hide them when building the collection.
Try doing this and let us know if you get stuck and we can go over it closer. Screenshots might help.
Some tools will allow you to select individual datasets to form a pair, and others like this one expect the data to already be in a collection folder (this keeps track of samples to avoid mixups). Later on, workflows will be the same way, with an expected input, usually a collection. With one sample all is about the same, but with several hundred (or thousand!), the collections are much easier to work with.
Next time, you can set up the collection at very start (after Upload), run though the QA steps, then use downstream tools all with the data organized.
This topic is another good reference and includes a workflow you can use (or modify) for these early QA steps. All the data is processed in a “collection” folder format, and you can see the different types of collection folders and how those are transformed from one into another in the hidden datasets/steps. All was done with the Collection Operations tools that first tutorial above is explaining.
Example output of the workflow included there (you can just navigate around in the History preview to see the “nested” formats, no need to import it, but of the Workflow might be helpful for later):
