Platform for Drug Discovery


Run analyses and status check


Table of contents


Run an analysis after an input choice


    In a case one input pipeline

    1. Open a project on which analyses are running.
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    2. Click analysis button on which red 'f(x)' is printed, after click an input data from a 'Project – Detail' view.
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      • In this case a single-end fastq format sequence file is chosen.
    3. Please choose a pipeline you want to use from a pipeline list.
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      • Numbers in brackets like '(1)' in the category list means the number of selectable pipeline, which depend on the data type of selected input data.
      • In this case select 'FastQC (SE)' pipeline from categories 'Tools'-'Quality control'-'Sequence QC'. Here 'SE' means single-ended and FastQC is a quality control tool provided by Babraham Bioinformatics.
      • Note that the number of listed pipelines is different when you do not select an input data.
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        This image is a list of pipelines without choice of an input. Four FastQC pipelines for four different input formats are listed.
        Only FastQC (SE) for single-end fastq pipeline is listed when the data which dataset type is 'fastq (single-end)' is chosen.
    4. Please confirm selected inputs and a project on which this analysis run.
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      • You can retry choice of inputs and choice of a project.
      • When you start analysis without choice of inputs or without choice of a project, you have to choose in this step.

    Run or Set option and run

      • After confirmation, you can choose 'Run' immediately with default option or 'Set option and run'.
    1. In a case immediately default option 'run' is clicked
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      • After you click the 'run' button, the screen transits to 'Analysis Status' view from 'Analysis Input and Output' view. This is the end of a running analysis process.
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    2. In a case 'Set option and run' is clicked
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      • After you click the 'Set option and run' button, 'Analysis - Option' view will appear.
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        *
        snip
        *
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      • Here you can select a FastQC version from a select box at a top, and you can set other options at a free text option input area at a bottom.
      • You can set several options separated by space characters. See the usage about available options in the option description.
      • On the contrary you cannot use file path, special characters like ('&', '(', ')', ';', '`', '|' and etc.) and the reserved options described in the option description.
      • If you are not an experienced user, we recommend you do not fill any characters in this free text area.
      • This area is mainly for experienced bioinformaticians who can use command line execution of tools. Customized option tuned by these experienced bioinformaticians should be set. Anyone can use these customized options if it is available.
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      • After setting options, click 'Run' button at a bottom.
      • After you click the 'run' button, the screen transits to 'Analysis Status' view from 'Analysis - Option' view. This is the end of a running analysis process.
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      • See Check statuses of pipelines next.

Run analyses after multi input choice


    In a case one input pipeline run multi times

    • When you want to run several times at once, do the following steps.
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    • In this example, two fastq (single-end) data are in a project.
    • Click 'Select' button on the bottom of a data icon. Then a clipboard sub window is displayed.
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    • Click 'Select' button on the other data icon. Then the data is added to a list in the clipboard.
    • Note that these steps of data choice operations are identical to ‘In a case multi input pipeline’.
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    • Select a pipeline of which input number is only one. Here 'FastQC (SE)' is chosen.
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    • Confirm that there are two data 'DRR000560.fastq(DS00164687)' and 'DRR000561.fastq(DS00164688)' in a select box for an input fastq(single-end).
    • Click 'Set option and run' or 'run' button. Please see the difference of the two here.
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    • After clicking the 'Run' button, two analysis records are generated, which means you ran two running operations at once in these steps of operation.
    • These pipelines are executed in parallel.
    • Of course you can two or more inputs can be operated.
    • See Check statuses of pipelines next.

In a case multi input pipeline

    • When you want to run a multi input pipeline, do the following steps.
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    • In this example, two fastq (single-end) data are in a project.
    • Click 'Select' button on the bottom of a data icon. Then a clipboard sub window is displayed.
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    • Click 'Select' button on the other data icon. Then the data is added to a list in the clipboard.
    • Note that these steps of data choice operations are identical to ‘In a case one input pipeline run multi times’.
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    • Select a pipeline of which input number is more than two. Here ‘mergeFASTQ (SE) max.10’ is chosen.
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    • Confirm the order of inputs.
    • You can replace the input order by drag-and-drop of input select boxes.
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        An image of drag-and-drop operation
    • Note that there are two asterisks '*' on input 1 and input 2. Which means input 1 and input 2 is required, but inputs from input 3 to input 10 are optional. This pipeline requires two or more inputs.
    • Click 'Set option and run' or 'run' button. Please see the difference of the two here.
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    • After clicking the ‘Run’ button, only one record is generated and two inputs are described in the ‘Input’ column of the record.
    • See Check statuses of pipelines next.