RAGE-redcap Data and Sequence Import Instructions

This guide provides step-by-step instructions for preparing and importing metadata and sequence data into RAGE-redcap.

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1. Metadata Import

Download Import Template

1. Go to Applications > Data Import Tool in REDCap.
2. Click Download Your Data Import Template to get the Excel template.

Complete Template

• Fill in the template using the latest data dictionary as reference.
• Adhere to approved choices for dropdown or radio fields; only these will be accepted by the database.
• Not all fields are relevant for every user — complete what applies.
• Latest data dictionary can be obtained:
  • From REDCap: Project Home > Design > Download Data Dictionary
  • From GitHub: RAGE REDCap Data Dictionary

Prepare Metadata

1. Save the completed template with a suitable filename.
2. Use the rabvRedcapProcessing R tool to prepare the data for REDCap import: rabvRedcapProcessing GitHub
3. Run the checkScripts.R script to process your imported sheet and generate sequencing and diagnostic forms ready for REDCap: checkScripts.R
   • Edit only the input file paths to match your data.
4. Visually inspect the outputs.

Important Notes

• Duplicate sequencing events: Carefully check your import list against the latest REDCap dataset to identify any repeat sequencing events. Manually adjust the redcap_repeat_instance for these repeats and remove duplicates from the diagnostic sheet to prevent overwriting existing records. Assign repeat instances in the new data consistently to ensure accurate tracking and integration.
• Review REDCap import warnings carefully; data that may be overwritten is highlighted in red.

Import Metadata

1. Go to Applications > Data Import Tool.
2. Select your import file (one at a time for diagnostic and sequencing forms).
3. Leave other settings as default and click Upload File.
4. Verify the import summary and confirm.

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2. Sequence Data Import

Prepare Environment

Before running the sequence import scripts, set up the conda environment included in this repository.

1. Create the environment from the provided environment.yml file:

   conda env create -f environment.yml
   

2. Activate the environment:

   conda activate rage-redcap
   

3. Verify installation:

   python --version
   

   Prepare Sequences

4. Ensure metadata has been imported first to associate sequences with records.
5. Obtain consensus FASTA sequences from your latest run.
6. Concatenate sequences from artic-rabv pipeline output: results/concatenate/concat_genome.fasta.

Split and Rename FASTA Files

1. Use multi_to_single_fasta.py to split the multi-FASTA into individual FASTA files: python3 multi_to_single_fasta.py
2. Edit input/output paths in the script as required.
3. Ensure filenames correspond to sample IDs from FASTA headers.
4. Negative controls: Copy and rename manually as negative_runname__runname__instance1.fasta and edit internal FASTA headers to match.

Match Metadata and Rename for Import

1. Run redcap-prepareFASTA.R
   • Edit metadata_file, fasta_dir, and output_dir filepaths.
   • Script matches sequences to REDCap metadata and renames FASTA files as sampleID__runname__instanceX.fasta.
2. Verify all renamed FASTA files and negative controls.

Upload Sequences to REDCap

1. Use bulk_upload_fasta_repeatInstances.py: python3 bulk_upload_fasta_repeatInstances.py
2. Edit input folder path to the renamed FASTA directory.
3. Ensure the REDCap API URL points to the correct project version (updates may change the endpoint).
4. Monitor command-line output for successful uploads.
5. If files do not appear, check API version and repeat instances.

Additional Notes

• Always verify sequencing records are not accidentally overwritten.
• Assumes you have REDCap API access with local environment files; contact project lead if not set up.
• REDCap provides informative error messages during import; use these to correct formatting or repeat instance issues before re-importing.