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Cell Ranger


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-5.0.0/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 \

For Targeted Gene Expression data, targeted UMI filtering is performed after the usual UMI Counting step. This additional filtering is only active for sequencing libraries with very high depth, in which spurious molecules can be observed in a very small fraction of reads. Targeted UMI filtering can be disabled when --target-panel is used with the --no-target-umi-filter flag, although this is not recommended.

The outputs of the pipeline will be contained in a folder named with the run ID you specified (e.g. sample345). The subfolder named outs/ will contain the main pipeline outputs.

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-5.0.0, then the target panel CSVs will be contained in /opt/cellranger-5.0.0/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.