Uploading with the Web Interface

This is a quick tutorial on how to upload data to IRIDA using the web interface. You should only upload data to IRIDA from the web interface if you are uploading sequencing data for a very small number of samples – uploading large amounts of data (especially if you’re a sequencing facility) should be done using the Illumina MiSeq uploader tool.

You should start from the beginning of this tutorial if you have not yet created a project, or your project does not have any samples. You can skip ahead to other sections if you’ve already got a project with samples added.

Creating a new Project

You can create a new project by clicking on the “Projects” menu at the top of the dashboard and selecting “Create New Project”:

Create new project dashboard location.

When you create a new project, you’ll need to provide a project name, and can optionally provide a project organism, a free-form project description, and a link to another web site that has more inforamtion about the project:

Create new project form.

A project name must be at least 5 characters long, and must not contain any of the following characters: ? ( ) [ ] / \ = + < > : ; " , * ^ | &

If you choose to set a project organism, click on the “Select an Organism” drop-down menu and begin typing the name of the organism. For example, if you wanted to specify a project organism of “Salmonella enterica”, you would begin to type “Sal” and the menu would allow you to choose from a set of well-defined organism names:

Project organism entry.

The organism names are derived from the NCBI taxonomy database.

To enable automated assemblies for the project, check the “Automatically assemble data uploaded to project” box. This setting will perform an assembly on all sequence files uploaded to this project. For more information about automated assemblies see the samples documentation.

When you’ve finished entering the details for your new project, click on the “Create Project” button. You will be redirected to the projects list.

IRIDA will automatically generate a numeric project identifier for your project. The project identifier is used by external tools for uploading sequencing data to IRIDA. The project identifier can be found in the “Project Details” panel, or in the projects list.

Creating a project from cart

You can create a project with samples already added to the project by using the cart. To use this feature, you must first add some samples to the cart. Once the samples are added you can click the arrow next to Select a Pipeline, and click Create Project from Samples. This will bring you to the create project page.

Create project cart

Continue creating the project details as described above, but note the checkbox Add samples in cart to project. If this checkbox is enabled any samples in the cart will be automatically added to this project. If there are any samples which you cannot add to the project, a warning will be displayed below.

Create project cart warning

Creating a Sample in your Project

You can add a new sample to the project if you have the project Manager role on the project. To add a new sample to the project, click on the “Add New Sample” button in the “Samples” menu:

New sample button

Clicking this button will take you to the Create New Sample page. When creating a sample, you must define the sample name (only upper and lowercase letters, numbers, and the special characters !, @, #, $, %, _, -, and ` are allowed) and optionally choose an organism for the sample:

Create new sample palge

If you choose to set a sample organism, click on the “Organism” drop-down menu and begin typing the name of the organism. For example, if you wanted to specify a sample organism of “Escherichia coli O26:NM”, you would begin to type “Esc” and the menu would allow you to choose from a set of well-defined organism names:

Taxonomic terms

When you’ve finished choosing the name and organism for the sample, click on the “Create Sample” button.

Create Sample

Uploading data to your Sample

Sequence files can be uploaded by clicking on the “Upload Sequence Files” button, on the left hand side side of the sequence file table. Files must have the extension .fastq or .fastq.gz, all other formats will be ignored.

Upload sequence file.

You can select single or multiple files in the system file selection window.

Upload File Selection.

Files will upload immediately and a progress bar will be displayed. If you need to cancel an upload click the Cancel Upload Button button.

Cancel upload