This guide explains how to upload datasets and generate reports.
Navigate to the home page and click New Report in the top right corner. This will take you to the New Report page.
The page is divided into three sections. Work through them top to bottom.
The first section covers general aspects of the experiment that determine how your data will be processed.
[COMING SOON].Scroll down to the Samples section. Use this section to upload FCS files and assign them to keyword groups. These groups set up the statistical comparisons performed later.
Click Upload Folder to upload an entire folder or Upload Files to select individual files. Navigate to your files and click Open. Repeat the process to add more files.
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Do I have to clean up my files?
Upload clean, compensated FCS files (e.g., live, singlet, CD3+ T cells). Clean up files in your preferred gating software and export the target population for downstream analysis. You do not need to rescale your data.
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terraFlow automatically assigns sample keywords based on file names and folder structure. Scan the table to make sure keyword assignments are correct.
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How does terraFlow know what keywords to assign?
terraFlow first looks for subfolders within your upload. It then looks for repeating keywords in the file names. Keywords must be separated by an underscore or other punctuation, as in 001_Day0_HighDose.fcs.
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Scroll up to the Manage Keywords section to change or add keywords. Enter the keyword name followed by possible values. Then click Save.
After clicking Save in the example above, the columns Timepoint and Dose will appear in the samples table. User the dropdown menu to assign keyword values to individual samples.
If a file fails to upload, an error message will appear in the top right corner and a Red Error Icon will appear in the last column of the samples table. Hover over the icon to delete the sample and try again.
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Pro tip for faster editing
Use the Enter, Tab, and Arrow keys to navigate the keyword and sample tables. When you change a keyword, a small blue handle will appear at the bottom of the cell. Drag the handle up or down to copy that keyword across multiple samples.
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If you’ve already annotated your files in a separate CSV or Excel file, click Upload Labels and navigate to your file. File must include one column with file names and one or more columns with sample keywords. Columns can have any name.
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How does terraFlow match my labels?
terraFlow scans your file for rows containing upload file names. Then, it looks for columns that group those files together. Columns that are unique to each file are automatically excluded.
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If you have negative gating controls (FMOs or FMMs), click Upload Files and select your control files. In the samples table, use the Gating Control dropdown to select omitted channels.
Gating controls will be used as references during gating. They will not appear in the final report.
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Pro tip
Put the detector or marker name in the file name to automatically match controls to channels. For example, FMO_B515.fcs or FMO_CD4.fcs.
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Scroll down to the Channels section. terraFlow automatically extracts channel metadata from the FCS file. Scan the table and make adjustments as needed.
terraFlow automatically excludes non-analytical channels like Time or Scatter. Turn off any other channels you don’t want to include in the group comparisons. For example, if you already pregated on CD3+ T cells, you would turn off the CD3 channel. Click the icon in the Include column to toggle channels on or off.
Check the Marker column for typos or errors. Click on the marker name to make changes. After you change the name, terraFlow will update the corresponding ID value. This value will be used to find papers with similar markers, even if they have a different name.