Processing 10x Genomics Visium spatial transcriptomics data
Background
10x Genomics provides the Visium platform for spatial transcriptomics.
This document outlines using the auto-process-ngs pipeline to
perform Fastq generation and QC for various types of Visium data.
Requirements
10x Genomics’ SpaceRanger software is used for Fastq generation for Visium data. It should be downloaded and installed before running the pipeline. No additional external software is required for the QC.
Fastq generation
If a sample sheet with the appropriate 10x Genomics indexes is provided
then all Visium data should be processed using the 10x_visium protocol
with the make_fastqs command, for example:
auto_process.py make_fastqs --protocol=10x_visium
This protocol wraps the spaceranger mkfastq command.
Note
If the sample sheet contains Illumina index sequences then the
standard protocol should be used instead (note that in this case
the defaults used for masking and trimming compared to the defaults
may differ from those used by SpaceRanger).
Analysis project setup and QC
Once Fastqs have been successfully generated, the SC_platform
and Library metadata items should be set to the appropriate values
for the Visium project(s) in the projects.info control file.
The following values are valid options for spatial data:
Single cell platform |
Library types |
|---|---|
|
|
|
|
Note
Although 10xGenomics Visium data are not single cell data, for historical reasons the platform information is currently being stored in the single cell platform metadata field.
Running the setup_analysis_dirs command will automatically transfer these values into the Visium project metadata on creation.
The run_qc command will then determine the appropriate QC protocol to use based on the metadata values.
Image data
The setup_analysis_dirs command also creates an empty
Visium_images subdirectory within the project, which should
either be populated manually with the corresponding image files,
or else be deleted.
Note
The presence of an empty images directory will cause the final archiving to stop with an error (as a reminder to copy in the associated images).