Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
This document describes the output produced by the pipeline. Most of the output is contained within HTML reports created with Quarto, but there are also other files which you can either take and analyse further by yourself or explore interactively with e.g. TissUUmaps.
The directories listed below will be created in the results directory after the
pipeline has finished. Results for individual samples will be created in
subdirectories following the
<OUTDIR>/<SAMPLE>/ structure. All paths are
relative to the top-level results directory.
The pipeline is built using Nextflow and processes data using the following steps:
- Space Ranger
- Workflow reporting
- Pipeline information - Report metrics generated during the workflow execution
outs/spatial/tissue_[hi/low]res_image.png: High and low resolution images.
outs/spatial/tissue_positions_list.csv: Spot barcodes and their array positions.
outs/spatial/scalefactors_json.json: Scale conversion factors for the spots.
outs/filtered_feature_bc_matrix/barcodes.tsv.gz: List of barcode IDs.
outs/filtered_feature_bc_matrix/features.tsv.gz: List of feature IDs.
outs/filtered_feature_bc_matrix/matrix.mtx.gz: Matrix of UMIs, barcodes and features.
All files produced by Space Ranger are currently published as output of this pipeline, regardless if they’re being used downstream or not; you can find more information about these files at the 10X website.
st_adata_processed.h5ad: Filtered, normalised and clustered adata.
.h5ad format as processed by the pipeline, which can be used for
further downstream analyses if desired; unprocessed data is also present in this
file. It can also be used by the TissUUmaps
browser-based tool for visualisation and exploration, allowing you to delve into
the data in an interactive way.
Quality controls and filtering
st_quality_controls.html: HTML report.
Report containing analyses related to quality controls and filtering of spatial data. Spots are filtered based on total counts, number of expressed genes as well as presence in tissue; you can find more details in the report itself.
st_clustering.html: HTML report.
Report containing analyses related to normalisation, dimensionality reduction, clustering and spatial visualisation. Leiden clustering is currently the only option; you can find more details in the report itself.
st_spatial_de.html: HTML report.
st_spatial_de.csv: List of spatially differentially expressed genes.
Report containing analyses related to differential expression testing and spatially varying genes. The SpatialDE package is currently the only option for spatial testing; you can find more details in the report itself.
- Reports generated by Nextflow:
- Reports generated by the pipeline:
pipeline_report*files will only be present if the
--email_on_failparameter’s are used when running the pipeline.
- Reformatted samplesheet files used as input to the pipeline:
- Parameters used by the pipeline run:
- Reports generated by Nextflow:
Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.