How to get a known repeat region data from UCSC and upload it to Maser
Table of contents
- How to get a known repeat region data from UCSC and upload it to Maser
- About this page
- Get the repeat data from UCSC
- Upload data to Maser
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
- Access to UCSC Genome Bioinformatics page.
- Push link for "Table Browser" on the left side menu.
- Select download options and fill information to specify the download data type and format.
- You can also access from here.
- In this example genome version is GRCh37/hg19 of human.
- Check the followings.
output format BED output file "anyName.bed.gz" in this example "hg19.RepeatMasker.20131009.bed.gz" file type returned gzip compressed
- If the file format, compression algorithm and postfix in the file name are not coincide, uploading process or analysis process will fail.
- Push "get output" button.
- Push "get BED" button for downloading.
- After download you get the repeat data file with the name you specified.
Upload data to Maser
- For uploading the data to Maser, please see the manual page for uploading for detail.
- Push "Upload My Data" button on a project where you want to upload.
- Uploading protocol HTTP is easier for uploading this kind of small size data.
- Select the data type and fill the upload data properties.
- 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.
- 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.
- You can recognize the uploaded data icon on the bottom of the Project Detail view.
- Upload is completed.