Quick Start

After you log in, you can use the button next to your Recent data to access it directly.

To search for and download your data, go to the Data Browser and filter your data using the blue search/filtering bar near the top of the page.
You will see your Raw data by default but can access your Processed data (example: Alignments) by clicking on the Processed tab.
You can also organize your data in carts for sharing with collaboration groups or for downloading in bulk using wget or curl.

Searching for and Downloading Data

You can search for your data by Sample, Run ID, Project ID, Group or Submitter in the Data Browser using the blue search bar. You can also filter your results by file types by selecting the files you would like to view. The entry for each sample can be expanded for more details and control over the different file types available for that sample in the raw or processed data tabs.

You can download data either by clicking the buttons next to a file or by adding the file or group of files/samples to a cart and using our one-click wget commands to download the files in bulk. Buttons containing an eye are viewable text files.


  • Typing in partial sample names or IDs in the search boxes will also work.
  • Sample, Run ID, Project ID, Group or Submitter searches will apply across the Raw and Processed tabs but not the cart tab.
  • When you filter by File type in a tab, you can then select several samples and add that file type for all those samples to your selected cart using the green "Add selected" button. Note: File type filters are only applicable for the current tab.

The Cart

Carts can be used to organize your data for downloading and sharing. You will have access to a default cart that you can rename and share. You can also create new carts. You can add all the raw or processed files for a sample or individual files to a cart by clicking the button next to the sample in the Data Browser or the individual file after clicking the sample line to expand it.

Tip: To download a lot of files in one go, you can organize them in a cart and then use our convenience Get links button to get a wget command line or a list of links to the files you would like to download.

Data Sharing

You can share data by organizing it in a cart and sharing the cart within and/or between groups that you belong to. Please note however that whoever you share the data with must belong to groups that have access to the data to be able to access the data you have shared.

We can add access for collaborators to your existing PubShare group and/or create collaboration groups with subsets of your data and access to specific users. To arrange this, please contact us at

You can also provide collaborators temporary access to individual files by clicking on the button next to the file and generating a Public Link that you can share. Please note that these public links expire after 14 days.

Missing Data

This portal serves data from within the last two years. If you can not find your data after trying the available filters (Run, Project, Group, Submitter) and you have checked under both the "Raw" and "Processed" tabs, please click the button below to submit a missing data request.