Space Ranger2.0 (latest), printed on 11/22/2024
The spaceranger count pipeline for single-library analysis of fresh frozen (FF) and formalin-fixed paraffin embedded (FFPE) samples will each output the files described below in the outs/ directory. The file hierarchy of the subfolder outs/ will follow this structure:
outs ├── analysis │ ├── clustering │ ├── diffexp │ ├── pca │ ├── tsne │ └── umap ├── cloupe.cloupe ├── filtered_feature_bc_matrix │ ├── barcodes.tsv.gz │ ├── features.tsv.gz │ └── matrix.mtx.gz ├── filtered_feature_bc_matrix.h5 ├── metrics_summary.csv ├── molecule_info.h5 ├── possorted_genome_bam.bam --------| ├── possorted_genome_bam.bam.bai | [Optional outputs, disabled using --no-bam argument] ├── possorted_genome_bam.bam.csi --------| ├── probe_set.csv [For FFPE samples or CytAssist processed Fresh Frozen samples] ├── raw_feature_bc_matrix │ ├── barcodes.tsv.gz │ ├── features.tsv.gz │ └── matrix.mtx.gz ├── raw_feature_bc_matrix.h5 ├── spatial │ ├── aligned_fiducials.jpg │ ├── aligned_tissue_image.jpg [CytAssist workflow only] │ ├── barcode_fluorescence_intensity.csv [For --darkimage fluorescence image input only] │ ├── cytassist_image.tiff [CytAssist workflow only] │ ├── detected_tissue_image.jpg │ ├── scalefactors_json.json │ ├── spatial_enrichment.csv │ ├── tissue_hires_image.png │ ├── tissue_lowres_image.png │ └── tissue_positions.csv └── web_summary.html
The table lists the output files within the outs/ subfolder indicating workflow specific files:
| File Name | Description |
|---|---|
web_summary.html | Run summary metrics and plots in HTML format, described in Web Summary |
cloupe.cloupe | Loupe Browser visualization and analysis file |
spatial/ | Folder containing outputs that capture the spatiality of the data. Learn more |
spatial/aligned_fiducials.jpg | Aligned fiducials QC image |
spatial/aligned_tissue_image.jpg | Aligned CytAssist and Microscope QC image. Present only for CytAssist workflow |
spatial/barcode_fluorescence_intensity.csv | CSV file containing the mean and standard deviation of fluorescence intensity for each spot and each channel. Present for fluorescence image input specified by --darkimage |
spatial/cytassist_image.tiff | Input CytAssist image in original resolution that can be used to rerun the pipeline. Present only for CytAssist workflow |
spatial/detected_tissue_image.jpg | Detected tissue QC image |
spatial/scalefactors_json.json | Scale conversion factors for spot diameter and coordinates at various image resolutions |
spatial/spatial_enrichment.csv | Feature spatial autocorrelation analysis using Moran's I in CSV format |
spatial/tissue_hires_image.png | Downsampled full resolution image. The image dimensions depend on the input image and slide version. |
spatial/tissue_lowres_image.png | Full resolution image downsampled to 600 pixels on the longest dimension |
spatial/tissue_positions.csv | CSV containing spot barcode, if the spot was called under (1) or out (0) of tissue, the array position, image pixel position x, and image pixel position y for the full resolution image |
analysis/ | Folder containing secondary analysis data including graph-based clustering and K-means clustering 2-10; differential gene expression between clusters; and PCA, t-SNE, and UMAP dimensionality reduction. Learn more |
metrics_summary.csv | Run summary metrics in CSV format, described in Gene Expression Metrics page. |
probe_set.csv | Copy of the input probe set reference CSV file. Present for Visium FFPE and CytAssist workflow |
possorted_genome_bam.bam | Indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, annotated with barcode information |
possorted_genome_bam.bam.bai | Index for possorted_genome_bam.bamIn cases where the reference transcriptome is generated from a genome with very long chromosomes (>512 Mbp), Space Ranger v2.0+ generates a possorted_genome_bam.bam.csi index file instead. |
filtered_feature_bc_matrix/ | Contains only tissue-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). |
filtered_feature_bc_matrix.h5 | Same information as filtered_feature_bc_matrix/ in HDF5 format. |
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. |
raw_feature_bc_matrix.h5 | Same information as raw_feature_bc_matrices/ in HDF5 format. |
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 |