Guide to Carts

Basic cart usage | Saving and sharing carts | Managing multiple carts | Tutorial video

Basic cart usage

ENCODE portal carts allow you to group an arbitrary set of experiments into a container. As with search-result pages, you can easily generate a list of downloadable URLs for all files in all experiments in your cart along with experimental metadata for all files you download.

Let’s start with the most basic form of carts in which they only exist in your browser window’s memory. Later we’ll look at logging in with a user account to save carts and share them with others.

Adding many experiments to your cart.

The search-results page has a convenient way to add many experiments to your cart at once.

Select experiment search results with the Search item under the Data menu
Selecting experiment search results

Any experiments in your search results displays a cart button to its right. Carts can only contain experiments and functional characterization experiments. Other types of items do not have a cart button to their right.

View of experiment search results with cart button highlighted

Carts can contain up to 4000 experiments, but a large number of experiments in your cart can cause certain operations to take a long time to complete. Filtering your experiments down to as small a set as possible helps keep the performance of cart operations high. The following example has the “eCLIP” filter selected which reduces the number of search results to 225 experiments.

After adding multiple experiments to a cart

With these 225 experiments selected, clicking the “Add all items to cart” button adds them to your cart, and a cart menu that shows the number of items in your cart appears next to the Help menu.

Viewing your cart

Choosing “View cart” from the cart menu takes you to the Cart page with the URL. Unlike most ENCODE portal URLs, this URL only shows your cart contents in this web browser window, and other people going to the same URL don’t see your cart but might see their own cart contents, and you don’t see these cart contents in a different browser window.

View of cart

Different views of your cart appear in the main portion of this page, while a set of file property filters appear on the left. These filters allow you to select a subset of your experiment’s files to view and download.

Datasets tab

The main portion of the Cart page initially displays a list of the experiments in your cart. You only see 25 experiments at a time, and the pager in the upper-right corner lets you move between the pages of 25 experiments. You can use the cart icons to immediately remove specific experiments from your cart.

The file property filters do not affect the contents of your Datasets tab. This tab simply displays a list of all experiments in your cart regardless of the files from those experiments that you have selected.

Genome browser tab

This view shows genome browser tracks for all files selected by the file property filters. Only files capable of visualization populate this tab. Selecting filters with a small visualization icon to their right selects files that appear in these tracks. If you only select filters with no visualization icon, no files appear in this view.

If you only have an interest in visualizable files, select the “Show visualizable data” checkbox above the filters so that only filters that select visualizable files appear.

Genome browser in cart view

Processed data tab

This view displays all processed data files in the experiments in your cart. All files in this view have assemblies, so you only see the files in the currently selected assembly filter.

Raw data tab

This view shows all files in the experiments in your cart that lack an assembly. The files in this view do not use the file property filters at all, so the filters appear grayed out while you have this tab selected.

Downloading files

You have three options for downloading the files from the experiments in your cart that you can select with the menu that appears when you click the arrow on the right.

The three cart download options
Cart download options

Processed data files option

This default option downloads all the files that appear in the “Processed data” tab, and are subject to all your selected filters.

Raw data files only option

This option downloads all the files that appear in the “Raw data” tab. The selected filters do not affect this option.

All files option

This option downloads all the files in all experiments in the cart. The selected filters do not affect this option.


These three options decide what the download button does. So first choose one of these options from the menu, then click the button to its left to begin the process of downloading files. For any of the three options you choose, clicking the download button pops up a dialog box that gives you information about downloading all the selected files in all the experiments in your cart.

File download dialog

Once you click the “Download” button in the dialog box, a file called “files.txt” gets downloaded that contains the URLs of all the selected files, as well as a line to generate and download a “metadata.tsv” file that contains a listing of the same files along with their experimental metadata.

If you have more than 500 experiments in your cart, you also see the warning in red. Clicking the Download button when you have a large number of experiments in your cart can result in a long delay before the “files.txt” file begins downloading. During this delay, you can still use the portal, but buttons that modify your cart appear dimmed until “files.txt” has finished downloading.

Adding and removing individual experiments

In addition to adding multiple experiments to your cart and clearing your cart, you can also add and remove individual experiments.

As mentioned before, the search-results page shows a cart button to the right of experiments. This button appears filled in for experiments currently in your cart, and as an outline for experiments not in your cart. Clicking the cart button of an experiment in your cart removes it from the cart, and the button appears as an outline. Clicking the cart button of an experiment not in your cart adds it to your cart, and the button appears filled in.

You can also add and remove experiments on individual experiment pages using a button above the summary.

Add to cart button on an experiment

Clearing your cart

Once you no longer need your cart, click the “Clear cart” button on your cart page. You get a chance to back out of this action, or to continue. Once you clear your cart, you cannot bring its contents back.

Another way to clear your cart involves clearing your browser window’s memory by reloading the browser or visiting another website while you have items in your cart. When you do this, you see a generic alert that lets you back out of clearing your browser window’s memory in case you do this by accident.

Saving and sharing carts with user accounts

Carts have more abilities when you have signed in with your user account on the ENCODE portal, including:

  • Saving your carts so they can be recalled
  • Sharing saved carts with others
  • Adding more than 4000 items to your carts, with a corresponding performance penalty on the cart page as you add more items

The following sections describe additional cart abilities when you have signed in.

Members of the ENCODE consortium often have user accounts assigned to them. But anyone can create an account to take advantage of the features with a cart you can save. See the section “Creating a new user account” below.

Saving your cart

Once you have logged in with your ENCODE portal user account, carts automatically get saved to the ENCODE portal as you add and remove items — you don’t need to specifically save your cart. You can view your carts on different browsers and computers, and you don’t lose this cart by reloading the browser window or going to a different website.

Sharing your cart

You can share your cart with others through the “Share cart” item in your cart menu.

Selecting Share cart menu, including your default cart name

Selecting this item brings up a dialog box that lets you copy the unique URL to your cart. Others who visit this URL can see the contents of your cart, though they cannot modify your cart — only you can modify your own cart.

Notice this cart also has a name — “Lorem Ipsum cart” in this case for the user “Lorem Ipsum.” We’ll look at cart names in more detail below.

Creating a new user account

Anyone wanting to take advantage of cart features associated with an ENCODE portal user account can create a new user account themselves. Scroll to the bottom of any page on the ENCODE portal and click the “Sign in” link.

A pop-up appears with four login service options. Choose a service on which you already have an account and follow their sign-in instructions. When a message appears that says, “You are about to create an ENCODE account…” click the “Proceed” button. This creates your account and automatically signs you in. You can sign in with that account in the future.

You can tell you have signed in if your name from that login service appears next to the search box at the top of the page. You can sign out at any time by choosing the “Sign out” option in the menu that appears when you hover over your name or click on it.

Managing multiple carts

Logged-in users can have up to 30 independent carts, each containing its own set of experiments that can overlap with your other carts’ sets of experiments. You set one of your carts as the “current cart,” and all of the operations described above apply to that cart until you set another of your carts as the current cart.

Each cart has a name that must be unique among all your carts. You can also optionally assign an identifier to each cart that you can use in the URL for your cart when you share it. This identifier must be unique among all carts in the system, even if they belong to other users.

Every user gets one cart initially with a name starting with that user’s name. In the example given below, user “Lorem Ipsum” has an initial cart called “Lorem Ipsum cart.”

Cart Manager

When logged in, choose the “Cart manager” option from the cart menu which brings up a page showing a list of all the carts belonging to you.

The cart manager as it appears with the initial cart

Adding a new cart

To add new carts, click the New cart button at the upper-right corner of the list. This brings up a modal that lets you specify the name and optional identifier for the new cart.

New cart dialog box

The notes below each field describe the limitations for the name and identifier. The arrow button in the middle lets you toggle automatic-transfer mode, so clicking it enables the automatic transfer of the name you enter to the identifier (the button appears with a dark background) and clicking this button again disables automatic transfer. While you have automatic transfer enabled, anything you type into the name field gets copied to the identifier field but modified to work better as a part of a URL, so spaces get converted to dashes, and anything not a standard letter or number gets converted to dashes or ignored depending on what those characters are. You can also type directly into the identifier field, with the same limitations on the kinds of characters you can enter.

Once you feel satisfied with the name and optional identifier, click the New cart button to create this cart, and you then see your new cart in your list of carts. If you had left the identifier field blank, the new cart has all the same abilities as any other cart but it gets an automatically assigned identifier.

Setting the current cart

You only work with one cart at a time, so you need to set one of your carts as the “current cart.” You do this in the cart manager by clicking the button in the Current column on the right side of the cart’s line in the list of carts, which also highlights that cart in blue. Once you do that, all cart operations — adding to the cart, viewing the cart, downloading the cart’s files, etc. — apply to that cart.

While all your carts and their contents are part of the ENCODE database, your web browser keeps track of the current cart. If you switch to a different browser or a different computer, you could see a different cart set as the current cart.

The current cart selected and reflected in the cart menu

Renaming, sharing, and deleting carts

The Actions column of the cart manager has the three operations you can perform on a cart: rename, share, and delete.

Renaming a cart brings up the same dialog box as creating a new cart and gives you the same options.

Sharing a cart brings up the same dialog box as sharing a cart from the cart menu. However, you can share any cart with the cart manager whether the current cart or other carts.

When you delete a cart and confirm that you mean to delete it, you can no longer retrieve that cart. Deleting a cart also frees its identifier if it had one — its identifier becomes available for other carts. You cannot delete the current cart; to delete a cart you have to set a different cart as the current cart first.

Auto Save carts

If you haven’t logged in and you start collecting items into a cart and then you log in, those items automatically get saved to a special cart called “Auto Save” that appears in yellow in the cart manager. This cart has no identifier, and you cannot rename it, share it from the cart manager, or set it as the current cart.

You can merge the auto-save cart’s contents into your current cart. To do this, go to the cart manager and make sure you have set the cart you want to merge the auto-save cart’s items into as the current cart. Then click the “Auto Save” cart’s link in the list to view the auto-save cart’s contents. Above the contents you find the “Add to current cart” button. When you click this button, all the contents of the auto-save cart get merged into the current cart, without duplicates.

You never have more than one auto-save cart, so if you already have one and you log in again with items in the logged-out cart, those new items get merged into your existing auto-save cart’s items.

Tutorial videos