Before you begin your Space Ranger run, you will need to prepare the input files. These files will vary depending on the parameters of your experiment, the assay chosen, and which Space Ranger pipeline you are using.
Prepare your Space Ranger inputs based on the following considerations:
- Which Space Ranger pipeline are you using? The input files differ between
spaceranger countandspaceranger aggr, for example. See Choosing a pipeline. - How are you generating your FASTQ files? If you are starting from BCL files right off the sequencer, you have the option of using spaceranger mkfastq, or direct demultipexing with Illumina software. If you already have FASTQ files, but are unsure of how they were generated, you may wish to visit Specifying Input FASTQs. It may also be helpful to brush up on your sequencing recommendations for Visium libraries.
- Next, you will need to consider the image inputs that you used.
- The pipeline requires some details about the slides. For more information, see the Slide Parameters page. We also have instructions for downloading a slide file for local operation when running Space Ranger without access to the internet.
- For fluorescence images or cases where the fiducial markers are obstructed or tissue boundaries are unclear, manual fiducial alignment for Direct Placement or Manual CytAssist Image Alignment may be necessary.
- To analyze Protein Expression data, you will need the Feature Reference CSV.
- Finally, remember to visit the Download Center to download Space Ranger and the pre-built references.
Questions or concerns about tracking down your inputs for your Space Ranger run? Contact [email protected].