Help

To run a SPEEDI analysis using this website, you will first need to provide the following information:

  • Analysis Title: This is the name that will be used for your analysis results in our system. Choose a title that accurately describes your data!
  • Email: This is the email address where we will send a link to your analysis results.
  • Species: Species associated with your data (Human or Mouse).
  • Data Type: How were your data generated? Options include scRNA, scATAC, Paired Sample (scRNA + scATAC), and True Multiome (scRNA + scATAC). Paired sample data refer to scRNA and scATAC coming from the same aliquot, while true multiome data refer to scRNA and scATAC coming from the same cell.
  • Reference Tissue: Reference tissue type (used to map cell types via reference). Certain reference tissues are only available for mapping to scRNA data. However, we also make these reference tissues available for the true multiome option, as we can transfer the cell type labels from the scRNA data to the same cells in the scATAC data.

After filling out the above information, click the Save Options button.

Next, you will upload your sample data. Your data must be archived in a .tar.gz or .zip file for processing.

Ideally, your archive will contain a set of folders (named after your samples), with each folder containing the data files for that sample. However, regardless of how you package your data, SPEEDI will try to find your sample data and assign reasonable sample names.

For scRNA, sample data should be filtered data generated by Cell Ranger in the MEX format. SPEEDI also works with H5 format files. If working with MEX files, sample data should always follow the standard naming convention (three files with names barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz). If working with H5 files, sample data file names should always end with filtered_feature_bc_matrix.h5. For example, "filtered_feature_bc_matrix.h5" and "Sample_1_filtered_feature_bc_matrix.h5" would both be fine, but "filtered_matrix.h5" would result in an error.

For scATAC, sample data should be fragment files (.tsv.gz) generated by Cell Ranger. Optionally, you can also include the associated tabix index files (.tsv.gz.tbi).

If you are processing paired sample or true multiome data, both scRNA and scATAC data files should be stored in the same sample folder.

Select your sample data archive by clicking the "Choose File" button. Then, click the "Upload Data and Begin SPEEDI Analysis" button to upload your data and launch your SPEEDI analysis job. You will receive an email when your analysis is complete.

If you have any questions about SPEEDI, please contact a SPEEDI administrator (speedi 'at' genomics.princeton.edu).