Platform for Drug Discovery

How to get a known repeat region data from UCSC and upload it to Maser

Table of contents

About this page

  • You can get RepeatMasker annotation data for a specific genome version from UCSC table browser.
  • This description explains how to get known repeat information as a BED format.

Get the repeat data from UCSC

  1. Access to UCSC Genome Bioinformatics page.
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    • Push link for "Table Browser" on the left side menu.
  2. Select download options and fill information to specify the download data type and format.
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    • You can also access from here.
    • In this example genome version is GRCh37/hg19 of human.
    • Check the followings.
      output formatBED
      output file"anyName.bed.gz"in this example "hg19.RepeatMasker.20131009.bed.gz"
      file type returnedgzip compressed
    • If the file format, compression algorithm and postfix in the file name are not coincide, uploading process or analysis process will fail.
  3. Push "get output" button.
  4. Push "get BED" button for downloading.
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    • After download you get the repeat data file with the name you specified.
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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 label for identification you want.
    • Data Type:The data type must be BED.
    • 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 several tens of 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.