Genome

A genome is required for all spatial analyses. The input must be a TAR.GZ containing a genome FASTA and annotation GTF.

Default Genomes

Spatial-specific Mouse and Human genomes are provided in the genome_bundle:

• /genomes/mm39.tar.gz
• /genomes/hg38.tar.gz

These genomes are available by default for auto-launch and manual launch analysis.

Custom Genomes

DRAGEN StrataMap supports inputting custom genomes as long as a valid genome annotation file (GTF) and genome (FASTA) are provided. There are two options for producing the genome reference:

1. Contact support and provide the genome (FASTA) and genome annotation file (GTF) for the desired custom genome, and support will send back a genome in the correct format.
2. Use the DRAGEN Reference Builder along with a few manual steps. DRAGEN StrataMap supports custom genome usage via this method.

Prerequisites:

• A genome FASTA
• A genome annotation file (GTF), gzipped (example: GENTEST.gtf.gz)

  • It cannot be named genes.gtf.gz

1. Upload your .gtf.gz and .fa files to the Sequence Hub.

   1. Navigate to Projects.
   2. Create a new project if necessary.
   3. Upload the .gtf.gz and .fa files to the project.
2. Navigate to Apps in the Sequence Hub and search for "DRAGEN Reference Builder".

   
3. Launch the 4.5.4000 version of the App.
4. Populate the fields in the App with the uploaded files and any other required information, and click Launch Application. Ensure you input the FASTA file and click the "RNA" box to include the GTF file. Example:
5. Once the application has completed, download the .tar.gz by navigating to the project and selecting the completed analysis. Next, click on the files icon > download > Analysis. This will bring up the following pop-up menu with instructions to download using the BaseSpace Sequence Hub Downloader.
6. Finally, upload the tar.gz to Core using the Core UI or the icav2 command-line tool.

• If using the UI, navigate to the project > data > folder you wish to upload the file to, then drag and drop the file into the designated location.

1. At this point, the .tar.gz is available and may be selected as the genome for manual execution of the DRAGEN StrataMap analysis.

Local Custom Genome

If running DRAGEN StrataMap locally, follow the instructions for creating a custom genome, ending on step 5, which will provide the genome to use locally.

Troubleshooting

• This process does not guarantee the efficacy of the genome for analysis, only correct formatting.
• If the genome is causing a problem in analysis, it will appear in the FastqFlow stage of analysis. Review the nextflow_issues.log found in the output files tab; it will include the error message.