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Overview
Here we list steps to download results and data generated after running samples through the mNGS Nanopore pipeline. We also describe how to navigate to the pipeline visualization where you can see details regarding the analysis workflow and download intermediate files.
After reading this guide, you will be able to:
Download data from Sample Report page
Learn about:
Download data for one or multiple samples (bulk download)
Learn about:
Download reads and contigs representing taxa of interest
Download raw and intermediate files
Navigate to the pipeline visualization
Downloading data for a single sample from Sample Report page
You can easily download data for a sample of interest. To do this:
1) Navigate to the Sample Report page for the sample of interest.
2) Click the Download button on the right-hand side of the page.
3) Select the file of interest from the Download dropdown menu.
Download dropdown menu. Note that you can only download a Report Table with Applied Filters after applying filters (See Filter Sample Report).
Files available to download from the Sample Report page
Downloading data for one or multiple samples (bulk download)
You can download reports for one or multiple samples from the Project page. Please note that files available through the Downloads page will be deleted after 7 days of creating the download.
To download data from the Project page:
1) Go to the Samples page for the project of interest and select the sample(s) for download. Click the Download icon on the right-hand side of the page.
Select samples to download from the Sample Table for the project of interest.
2) A dialog box will appear where you can select the file of interest. Select the file and click “Start Generating Download”.
Below we describe report and sequence data files available for download. Note that the file options differ from those available for download for a single sample through the Sample Report page.
Files available to download through the Samples page for a project of interest
The report files contain detailed information regarding sample quality and metrics for identified taxa. Below we describe results included within the Sample Overview, Sample Taxon, and Contig Summary reports.
Sample Overview Report
Sample Taxon Report
Contig Summary Report
Downloading reads and contigs representing taxa of interest
You can easily download read and contig sequences associated with taxa of interest. To download sequences:
1) Go to the Sample Report page and hover over a taxon of interest. This will enable the Download icon.You can download all the sequences associated with a genus or a specific species.
2) Click “Contigs FASTA” or “Reads FASTA” from the Download dropdown menu to download sequences associated with the taxon.
Downloading raw and intermediate files
You can download data files produced throughout the pipeline. You can find intermediate files through the Sample Report or Pipeline Visualization pages.
To view intermediate files through the Sample Report page:
1) Navigate to the Sample Report page for the sample of interest.
2) Click the Download button on the right-hand side of the page.
3) Select “View Results Folder” from the Download dropdown menu.
4) Once on the Results folder page, search for the file of interest. Click on the file to download.
Scroll down or search for a file of interest within the Results folder page.
Navigating to the pipeline visualization
You can view details regarding steps implemented for analyzing a given sample through the mNGS Nanopore pipeline visualization. You can also use the visualization to find and download intermediate files of interest.
To view the pipeline visualization:
1) Navigate to the Sample Report page for the sample of interest.
2) Click the Download button on the right-hand side of the page.
3) Select “View Pipeline Visualization” from the Download dropdown menu.
You can navigate to the Pipeline Visualization page through the Download dropdown menu found in the Sample Report page.
4) Click the “ONT mNGS Pipeline” button on the Pipeline Visualization page to open visualization.
5) Click on a step of interest from the pipeline visualization. A panel will open on the right-hand side of the page with information about the step as well as input and output files. Simply click on a file of interest to download.
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