Salmon Quant paired-end read entry

[jennaj]

Welcome @Mark_C

Hopefully we can help!

The idea is to always but pairs of reads together inside of a collection.

Collections are like smart folders. The organization is by sample, and the collection can contain one or many samples (single end or pairs of reads). The outputs will keep retain the per sample organization. This helps to avoid sample or end mixups. All the read datasets will be in the hidden tab where you can toggle to active use them individually for exploratory work.

There are two primary ways to get the data into a collection. You’ll be using the first but next time you can load the data this way and run through the upstream steps inside the collection. It makes processing 1000s of samples just like processing one.

History → Auto Build List

The video here shows how. → Why collections?

Upload → Collection

This allows you to process one or many samples through all of your steps together: QA, trimming, analysis, summary reports. This avoids sample mixups and much less clicking around.

@jennaj

And, I’ll just add that you can Upload data directly into a collection, too. This is built into the Upload tool now and routes directly to the collection builder. Most is automatic – just name the collection on the next screen. Creating a collection in the history is just another route but most people will load data this way at the start.

Collections are how to process a lot of data but being able to jump in for exploratory work is important too! Find all the datasets inside of the smart Collection folder in the Hidden tab.

Opt out

If you really don’t want to use a collection for some reason, all of the older original versions of tool forms are still available!

For your case, you’ll just need to go back one version to:

• Salmon quant Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads (Galaxy Version 1.10.1+galaxy2)

Below is another example for SPAdes. All tool forms have versions listed. Once a tool form is published, each version is immutable for reproducibility reasons. The parameters available will always be what was originally included!

If you check the versions of tools hosted at the different servers, you will likely notice that the US server and EU server are a bit different. The US server is pending an update and is hosting the 1.10.1+galaxy2 version right now but will soon update to the version hosted at the EU server. But the older versions will still be available at both.

@jennaj

we keep everything that was once available for reproducibility reasons! Very important! We don’t want to break anyone’s workflow! Either an actual workflow or just how you are using the tools.

The prior versions of the SPAdes tool can be navigated with the Versions menu at the top of the tool form. If you were using individual datasets for a pair before, one of these was likely what you were using.

The most recent with this type of input was 3.15.5+galaxy3. → FAQ: Changing the tool version

Tool panel → Collection Operations

The collection folders may be manipulated in both simple and sophisticated ways!

@jennaj

For just a few datasets, toggle into Hidden tab in the history. Click on the eye icon to hide or unhide each dataset, or you can use the multi-select to hide/unhide in a batch.

More ways to transform the shape is covered in here. → Hands-on: Using dataset collections / Using dataset collections / Using Galaxy and Managing your Data

Tool panel → Collection Operations is where these tools are. Each has a little graphic to show what is happening but please ask if there is anything else and I’ll try to help.

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That’s a lot of information but I see that others are asking about the same topic, so I wanted to bring everything together again in a summary. Thank’s for letting me answer with a bit more exposition! And please ask if anything is not clear – you are welcome to share back screenshots to help explain.

Let’s start there, thanks!