HOME  ›   pipelines
If your question is not answered here, please email us at:  ${email.software}

10x Genomics
Visium Spatial Gene Expression

Targeted Gene Expression Outputs

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.htmlRun summary metrics and charts in HTML format, described in Web SummaryContains additional Targeted Gene Expression metrics
metrics_summary.csvRun summary metrics in CSV format, described in Gene Expression Metrics page.Contains additional Targeted Gene Expression metrics
possorted_genome_bam.bamIndexed BAM file containing position-sorted reads aligned to the genome and transcriptome, annotated with barcode informationReads not analyzed due to high sequencing depth and subsampling are unmapped and indicated using the xf:i:32 tag
possorted_genome_bam.bam.baiIndex for possorted_genome_bam.bamGenerally unchanged
filtered_feature_bc_matrixContains 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.h5Same information as filtered_feature_bc_matrix/ in HDF5 format.Contains only targeted genes*
raw_feature_bc_matricesContains 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.h5Same information as raw_feature_bc_matrices/ in HDF5 format.Generally unchanged*
analysisFolder 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 moreSecondary analysis performed only on the targeted genes
molecule_info.h5Contains 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 moreGenerally unchanged*
cloupe.cloupeLoupe Browser visualization and analysis fileContains only targeted genes
target_panel.csvCopy of the input Target Panel CSV fileOnly 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 moreGenerally unchanged

* HDF5 files now contain indices of the targeted genes within the features HDF5 group.