Space Ranger2.0, printed on 11/22/2024
| After June 30, 2023, new Space Ranger releases will no longer support Targeted Gene Expression analysis. |
The output from a Targeted Gene Expression analysis is generally similar to output from non-targeted analysis — see the table below for a comprehensive list of differences. The primary changes are:
The raw feature-barcode matrices and molecule info H5 file still provide information about all genes.
| File Name | Description | Differences for Targeted Gene Expression |
|---|---|---|
web_summary.html | Run summary metrics and charts in HTML format, described in Web Summary | Contains additional Targeted Gene Expression metrics |
metrics_summary.csv | Run summary metrics in CSV format, described in Gene Expression Metrics page. | Contains additional Targeted Gene Expression metrics |
possorted_genome_bam.bam | Indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, annotated with barcode information | Reads not analyzed due to high sequencing depth and subsampling are unmapped and indicated using the xf:i:32 tag |
possorted_genome_bam.bam.bai | Index for possorted_genome_bam.bam | Generally unchanged |
filtered_feature_bc_matrix | Contains only spot-associated barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the Feature-Barcode Matrix page. This file can be input into third-party packages and allows users to wrangle the barcode-feature matrix (e.g. to filter outlier spots, run dimensionality reduction, normalize gene expression). | Contains only targeted genes |
filtered_feature_bc_matrix.h5 | Same information as filtered_feature_bc_matrix/ in HDF5 format. | Contains only targeted genes* |
raw_feature_bc_matrices | Contains all detected barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the Feature-Barcode Matrix page. | Generally unchanged |
raw_feature_bc_matrix.h5 | Same information as raw_feature_bc_matrices/ in HDF5 format. | Generally unchanged* |
analysis | Folder containing secondary analysis data including graph-based clusters and K-means clustering 2-10; differential gene expression between clusters; and PCA, t-SNE, and UMAP dimensionality reduction. Learn more | Secondary analysis performed only on the targeted genes |
molecule_info.h5 | Contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or protein barcode. This file is required for additional analysis spaceranger pipelines including aggr, targeted-compare and targeted-depth. Learn more | Generally unchanged* |
cloupe.cloupe | Loupe Browser visualization and analysis file | Contains only targeted genes |
target_panel.csv | Copy of the input Target Panel CSV file | Only present for Targeted Gene Expression data |
spatial/ | Directory containing QC images for aligned fiducials and detetected tissue in jpg format, scalefactors_json.json, high and low resolution versions of the input image in png format, barcode_fluorescence_intensity.csv, spatial_enrichment.csv and tissue_positions.csv files. Learn more | Generally unchanged |
* HDF5 files now contain indices of the targeted genes within the features HDF5 group.