Couldnt access .fsta

[jennaj]

Welcome @Abinaya_Subramanian

To work with ab1 files in Galaxy, please see this tutorial. In short, you’ll need to transform into a fastq format to use tools that function on reads. Be sure to see the workflow! → Hands-on: Clean and manage Sanger sequences from raw files to aligned consensus / Clean and manage Sanger sequences from raw files to aligned consensus / Sequence analysis

Then, for fsta, these are just plain text fasta files, correct? Galaxy hosts many tools that work with or produce fasta data.

It might be important to know that Galaxy tool forms perform a “metadata check” when screening a history for the potential input files appropriate for any particular input select field. This check is looking at the datatype format attribute the tool is expecting, then checking that attribute as assigned to datasets, and if these match – the tool recognizes that dataset and lists it as an available input option. If nothing is listed, either the kind of data appropriate for the tool is not in the history yet, or the data may be there but have the wrong datatype currently assigned.

The best way to get the datatype assigned to datasets is to allow Galaxy to auto-detect the datatype when originally loading the data. This ensures that the format assigned is correct, including the level of file compression. If the data is already loaded, you can try to re-detect the datatype too (pencil icon > Datatype). A few exotic file types may need a direct adjustment but common types shouldn’t and a wrong “guess” may indicate a content problem.

Here is an example for a tool we happened to talk about at this forum, but the general advice applies to any tool, so maybe helps?

@jennaj

This is happening with the input setting on the Kraken2 tool form? Like this?

If so, one of these is likely the problem:

1. The input reads are not in the active history. You can try refreshing your browser window, or clicking on the Home Galaxy icon in the top left corner, then switching to the history, before loading the tool form up again. Hands-on: Understanding Galaxy history system / Understanding Galaxy history system / Using Galaxy and Managing your Data
2. The reads are not assigned one of the supported datatype “accepted formats”. Illumina reads would be fastqsanger or fastqsangergz. If the reads do not have that datatype from the start, then you’ll need to correct it (maybe by reloading the data) then redoing the upstream QA steps (since these also also rely on the correct quality score scaling definition in the datatype). Getting Data into Galaxy
3. Your data is not in a collection yet. This tool expects a Collection of paired reads for the shape of the data, not individual files. FAQ: Datasets versus collections. Load your data up using the Collection tab in the Upload tool or create it after from data already in your history.

Galaxy introductions

A good simple overview of common NGS file types and how these are displayed in Galaxy can be found in this very brief reference-style tutorial. → Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses

And this is a small collection of tutorials to get oriented for common sequence analysis tasks such as mapping reads. → Learning Pathway: Introduction to Galaxy and Sequence analysis

---

Let’s start there, but please know we can follow up more after you get oriented! If you want to share back your current history then let us know which tool you are trying to use, that can help to narrow down the advice. Or, post back some screenshots? We’ll need to see the top of the tool form (tool name + version), the input area you are expecting a dataset to be listed in, and the dataset you want to input into that area (expanded, so that the datatype format metadata is shown, along with the peek view).

• How to get faster help with your question

Thanks!