Analysis

During analysis, fastq files are processed with Genestrip Web, and result files in CSV format are produced.

Genestrip Web offers 4 options for providing fastq files.
Three of these options are intended for advanced users and are briefly described on GitHub.

For beginners, the job type Analyze Upload File(s) is the most suitable, as described below.

Starting an Analysis Job

  1. Start GeneStrip Web.
  2. In the web interface, click on the Jobs tab.
  3. Under Edit Job:, click the Create button at the bottom right.
  4. Enter a name for the new job in the Name: field.
  5. Select an installed database for analysis under For Database:.
  6. Select Analysis of Upload File(s) under Job Type: (unless it is already preselected).
  7. You do not need to check the checkbox under With Read Classification: as a beginner. This provides advanced results that a beginner may initially overlook.
  8. Click Choose Files... to choose one or more fastq files for analysis. If you select multiple files, they will be analyzed together, and the corresponding data will be combined in one result. Fastq files have the extensions .fq, .fq.gz, .fastq, or .fastq.gz.
    If you select files that do not match the fastq format, the subsequent analysis will produce an error.
  9. Click Save. The Start button will now turn green and can be clicked.
  10. Click Start to begin the analysis.

Started Analysis Jobs

Once you click Start, the analysis job will begin after a few seconds. First, the appropriate database is loaded into memory, if it was not already needed for the previous analysis job. The loading process can take anywhere from a few seconds to several minutes, depending on the size of the database. Important: During this phase, no progress will be visible to you in the web interface.

Afterward, the fastq files will be processed. The system will show the progress of the job in terms of time and processed data in the job details, along with an estimated remaining time. Depending on the size of the fastq files and available computing resources, the processing may take anywhere from minutes to several hours.

Important: As long as an analysis job of the type Analysis of Upload File(s) is running, you must not:

  • close the browser,
  • close the browser tab with the Genestrip Web interface or
  • turn off your computer or put it into sleep mode.

Otherwise, the analysis will be automatically canceled, and you will receive an error message instead of the result, because the corresponding browser tab is responsible for reading the fastq files and passing them to Genestrip Web until all data has been processed.

Once the analysis job is finished, you can view the result by clicking View... in Genestrip Web to open it as a table in your browser. Alternatively, you can download the corresponding CSV file with the same content via the link next to it.

For a started analysis job, the Start button changes to Stop. With Stop, you can cancel the job at any time; however, it cannot be resumed afterward.

Important: In Genestrip Web, only one job of the type Analysis of Upload File(s) can be started at a time.

Canceled Jobs and Logs

A failed or canceled analysis job has the status Canceled. Under Log:, you can view and download the corresponding outputs of the core system for the selected job. Logs are also available for completed or started jobs.

Continue to “View Results” …