This tutorial assumes that you have uploaded samples to GobyWeb. Samples can be used to generate alignment, which in turn can be used for analysis.  Recall from the data flow figure shown in the Introduction tutorial that when you align a Sample, an AlignJob is created. The AlignJob contains the configuration that will be provided to the aligner when it is executed on the compute grid. The final result is an Alignment.

To see a list of all of the Samples that you have previously uploaded to GobyWeb as well as all of the Samples that other people have shared with you select “Uploaded samples” from the Browse menu.

The primary features of the List of Samples are

  1. The total number of samples you have access to
  2. The first column shows the names of the Samples
  3. The last column shows the owner of the Samples
  4. The Filter button allows you to “Filter” the Samples that are displayed. You can search for samples by name, reads length, etc.

If you have more samples that can fit within the grid, scroll the grid using the scrollbars to see all of the samples you have access to.

To align a sample, select one of the Samples by clicking on the name of the sample (in the first column) and you will be shown the “Show Sample” page for that Sample. To start an alignment (create an Alignment Job) for this sample, click the Align button.

After clicking the Align button, you will be presented with the “Align Sample” screen.

The notable features of the “Align Sample” page are

  1. The description. This is text that should be meaningful to you. It will be given to both the Alignment Job and the resulting Alignment.
  2. This section allows you to verify the Sample that will be aligned.
  3. This section allows you to select an aligner and configure options that are general across all aligner. Aligner specific options can also be found slightly further down the page.
  4. This section allows you to select the Reference that you will align your sample against. These References will all be for the Organism you specified for your Sample. If the reference you select is a “Transcript-” reference, you will be aligning against Transcripts instead of aligning against the entire genome (which is the default).
  5. Once you have verified your alignment configuration, click Create and an Alignment Job will be created

Once the Alignment Job is created it will be submitted to the cluster for processing. A running or queued Alignment Job will look like the following:

The notable features of the “Show Alignment Job” page while the Alignment Job is running on the cluster are

  1. You can see the job is “Submitted” which may mean it’s queued or running. You can periodically click the (refresh) button to refresh the page to monitor the status of your job.
  2. If you need to kill the job before it finishes, click here on the X.
  3. The Visual Status (and the Legend) gives you an idea of the current state of your job.

You should receive an email from GobyWeb both when the job is submitted to the cluster and when the job is complete.

After the Alignment Job has completed running, the “Show Alignment Job” page will look like:

Click the “View Alignment” (or find the Alignment by selecting “Completed alignments” from the Browse menu).

The notable features of the “Show Alignment” page are

  1. These files are the result of the alignment. You can click any of the to download the individual file or select the “-all-file.zip” file to download all of the above files in a single zip file.
  2. The Alignment Charts provide information about the alignment that can be useful in helping to determine the quality of the alignment.