Using the Wash U Epigenome Browser @ BioHPC

BioHPC hosts a mirror of Wash U epigenome browser inside the university network at: http://epigenome.biohpc.swmed.edu. It is an exact copy of the original Wash U epigenome browser. The website is only accessible by internal campus network or via VPN. Thus, it is suitable to work on private or sensitive data, that should not be exposed to the general public.

3homepage.PNG

Fig. The homepage of BioHPC’s mirror of Wash U epigenome browser

Upload file to lamella

Since the epigenome browser ask users to provide an URL for their data, we need first upload the file to lamella, and then generate the URL using lamella web interface (https://lamella.biohpc.swmed.edu).

Make sure you upload your file to BioHPC storage space. It is recommended that you upload it to /project or /work, since epigenome data may be too large for /home2 storage space.

 Create a shared link for file in lamella web interface

Go to lamella web interface, find your file for the epigenome browser, click on three dots at the end of the file, and click “Details”. It will pop up a panel of detailed information, click “sharing” tab below the file name, then select “Share a link”, and copy this link. Now, an important step to keep in mind: add /download at the end of this link, when putting into the WashU browser later. This will let the browser get the uploaded file itself, otherwise, it will only get a link to this file.

1bigwig_lamella.PNG             2share_link.PNG

 

Add custom track on the Wash U epigenome browse

Go to BioHPC website: http://epigenome.biohpc.swmed.edu . Say we have human data, then we click on the picture of Human hg19, select “Custom tracks”, and choose the corresponding data type. A bigwig file is used in this case.

4custom_track.PNG     5add_custom_type.PNG

 

Paste the lamella shared link, add /download at the end of the link, give a track name, like "demo", and click submit.

6upload_bigwig.PNG

 

The track "demo" is added successfully as shown below.

7epi_result.PNG

 

For more information and tutorials about Wash U genome browser, please check this page maintained by the team at Washington University in St. Louis.