Platform for Drug Discovery

How to get a known gene annotation data from UCSC and upload it to Maser

Table of contents

About this page

  • You can get known gene annotation data for a specific genome version from UCSC goldenPath download sites.
  • This description explains how to get known gene annotation data as a refFlat version genePred format.

Get the gene annotation from UCSC

  1. Access to UCSC Genome Bioinformatics page.
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    • Push link for "Downloads" on the left side menu.
  2. Find an organism you are interested in the list.
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  3. Push a link for "Annotation database".
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    • In this case hg19, GRCh37 is selected.
    • You can also select an older version genome hg18 at the below.
  4. Search "refFlat" in your browser in the download sites goldenPath.
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  5. Download "refFlat.txt.gz" from the file list.
    • We recommend to make a note the data update date on the right because the annotation data is updated several times a week and annotation version is recognized by this update date.
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    • I recommend you rename the file name so that you can identify the update date and genome version.
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Upload data to Maser

  1. Push "Upload My Data" button on a project where you want to upload.
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    • Uploading protocol HTTP is easier for uploading this kind of small size data.
  2. Select the data type and fill the upload data properties.
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    • Data Label: Give the data the lavel for identification you want.
    • Data Type: The data type must be genePred(refFlat).
    • Data File: Select the downloaded data on your computer.
  3. Push upload button.
    • After pushing the Upload button, file uploading and decompressing processes proceed.
    • After a few seconds, the uploading was finished.
    • Push "Open Project Detail window" button.
  4. You can recognize the uploaded data icon on the bottom of the Project Detail view.
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    • Upload is completed.