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10x Genomics
Chromium Single Cell Gene Expression

Targeted Gene Expression Analysis

Cell Ranger performs analysis of single-cell Targeted Gene Expression data with the cellranger count pipeline. Cell Ranger provides the same interface and features for both Targeted and Whole Transcriptome Analysis (WTA) Gene Expression data, as described in Single-Library Analysis with Cell Ranger.

To enable Targeted Gene Expression analysis in cellranger count, specify the relevant Target Panel CSV file using the --target-panel flag:

$ cd /home/jdoe/runs
$ cellranger count --id=sample345 \
                   --target-panel=/opt/cellranger-4.0.0/target_panels/immunology_v1.0_GRCh38-2020-A.target_panel.csv \
                   --transcriptome=/opt/refdata-gex-GRCh38-2020-A \
                   --fastqs=/home/jdoe/runs/HAWT7ADXX/outs/fastq_path \
                   --sample=mysample \
                   --expect-cells=1000 \
                   --localcores=8 \
                   --localmem=64

Target Panel CSV

Target Panel CSV files corresponding to predesigned gene panels can be found within the target_panels directory in the Cell Ranger package. For example, if you installed Cell Ranger to /opt/cellranger-4.0.0, then the target panel CSVs will be contained in /opt/cellranger-4.0.0/target_panels. These CSV files can also be downloaded on the Panel Selection page, along with more detailed information about each panel.

Detailed documentation on this file format can be found here, along with descriptions of all other downloads provided for target gene panels.

Output Files

The output from a Targeted Gene Expression analysis is generally very similar to output from non-targeted analysis—see the table below for a comprehensive list of differences. The primary changes are the addition of targeting metrics, and that all secondary analysis for targeted data is performed after removing non-targeted genes from the count matrix. Likewise, the filtered feature-barcode matrix files and Loupe Browser file do not include non-targeted gene counts. The raw feature-barcode matrices and molecule info H5 file still provide information about all genes.

File NameDescriptionDifferences for Targeted Gene Expression
web_summary.htmlRun summary metrics and charts in HTML formatContains additional Targeted Gene Expression metrics
metrics_summary.csvRun summary metrics in CSV formatContains additional Targeted Gene Expression metrics
possorted_genome_bam.bamReads aligned to the genome and transcriptome annotated with barcode informationThe xf tag now indicates whether a read was filtered by targeted UMI filtering
possorted_genome_bam.bam.baiIndex for possorted_genome_bam.bam
filtered_feature_bc_matrixFiltered feature-barcode matrices containing only cellular barcodes in MEX formatContains only targeted genes
filtered_feature_bc_matrix_h5.h5Filtered feature-barcode matrices containing only cellular barcodes in HDF5 formatContains only targeted genes*
raw_feature_bc_matricesUnfiltered feature-barcode matrices containing all barcodes in MEX format
raw_feature_bc_matrix_h5.h5Unfiltered feature-barcode matrices containing all barcodes in HDF5 formatGenerally unchanged*
analysisSecondary analysis data including dimensionality reduction, cell clustering, and differential expressionSecondary analysis performed only on the targeted genes
molecule_info.h5Molecule-level information used by cellranger aggr to aggregate samples into larger datasets.Generally unchanged*
cloupe.cloupeLoupe Browser visualization and analysis fileContains only targeted genes
target_panel.csvTarget Panel CSV fileOnly present for Targeted Gene Expression data
feature_reference.csv(Feature Barcode Only) Feature Reference CSV file

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