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
- Access to UCSC Genome Bioinformatics page.
- Push link for "Downloads" on the left side menu.
- Find an organism you are interested in the list.
- Push a link for "Annotation database".
- In this case hg19, GRCh37 is selected.
- You can also select an older version genome hg18 at the below.
- Search "refFlat" in your browser in the download sites goldenPath.
- 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.
- I recommend you rename the file name so that you can identify the update date and genome version.
Upload data to Maser
- 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 lavel for identification you want.
- Data Type: The data type must be genePred(refFlat).
- Data File: Select the downloaded data on your computer.
- 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.
- You can recognize the uploaded data icon on the bottom of the Project Detail view.
- Upload is completed.