Summary

This page describes the method by which you can search for a dataset using the NeMO Portal (portal.nemoarchive.org), that can be transferred to FireCloud for analysis.

This will include the following steps:

1. Navigate to Data section of NeMO Data Portal
2. Use faceted or advanced search to identify the datasets of interest
3. Add the files to the shopping cart
4. Download manifest file(s)

Step 1. Go to the NeMO Archive Portal

Please go to NeMO Portal (portal.nemoarchive.org). Here is what the site should look like.

site_figures/nemo_data_portal/nemo-archive-main-landing-page.png

Click on the "Data" tab at the top-left or the "Data" button to switch to the faceted data search page of the portal.

Step 2. Faceted Search

NeMO Data Portal provides a simple faceted search query to help identify data of interest. The facets are shown on the left hand side of the data portal. As you click on the facets the page dynamically updates the number of samples and files that match the criteria selected. The figure below shows the main data landing page.

site_figures/nemo_data_portal/nemo-archive-data-landing-page.png

Select the 10X library type from the facets (shown with red outline), this will update the display to show all files that are related to 10X library type including fastq files, BAM files, and count matrices. See figure below.

site_figures/nemo_data_portal/nemo-archive-data-select-library.png

Once you have selected the 10X library type, narrow down the files to just sequence files. Use the "File Counts by File Format" panel to select the "fastq" filetypes. To select the file type either click on the section of pie chart corresponding to file type by hovering over the chart, or use the table icon on the top right of the panel to display as table and select the appropriate file type.

site_figures/nemo_data_portal/nemo-archive-data-show-file-format.png

This will update the page to show fastq files generated from 10X libraries. Once you have narrowed down the data, click on the "Files" tab to show a list of files that match the search criterion.

site_figures/nemo_data_portal/nemo-archive-data-selected-fastq-file-format.png

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Step 3. Add To Shopping Cart

Once you have narrowed down your search to identify the datasets, you may click one or more of the files by clicking on the cart icon next to the file list, or choose all the files, and add them to the shopping cart.

site_figures/nemo_data_portal/nemo-add-to-shopping-cart.png

The shopping cart icon on the top right of the page will display the number of items currently in the cart.

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Step 4. Transfer Data to Terra

Click on the shopping cart to view the contents of the shopping cart. You can transfer the files to Terra which includes metadata for leveraging pipelines.

Click on the Terra button to transfer data. You may also optionally download the data and metadata with the download manifest option.

site_figures/nemo_data_portal/transfer_data_terra.png

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