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Cell Ranger


Loupe

10x Genomics
Chromium Single Cell Gene Expression

Cell Ranger7.1, printed on 11/05/2024

Targeted Gene Expression Outputs

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 name Description Differences for Targeted Gene Expression
analysis/ Folder containing the results of graph-based clusters and K-means clustering 2-10; differential gene expression analysis between clusters; and PCA, t-SNE, and UMAP dimensionality reduction. Learn more Secondary analysis performed only on the targeted genes
cloupe.cloupe A Loupe Browser visualization and analysis file. Contains only targeted genes
filtered_feature_bc_matrix/ Contains only detected cell-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 cells, 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*
metrics_summary.csv Run summary metrics file in CSV format, described in the Gene Expression metrics page. Contains additional Targeted Gene Expression metrics
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 Feature Barcode. This file is a required input to run cellranger aggr. Learn more Generally unchanged*
possorted_genome_bam.bam Indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, as well as unaligned reads, annotated with barcode information. Learn more The xf tag now indicates whether a read was filtered by targeted UMI filtering
possorted_genome_bam.bam.bai Index for possorted_genome_bam.bam
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_matrix in HDF5 format. Generally unchanged*
web_summary.html Run summary metrics and charts in HTML format, described in the count web summary page. Contains additional Targeted Gene Expression metrics
target_panel.csv Target Panel CSV file Only present for Targeted Gene Expression data
feature_reference (Feature Barcode Only) Feature Reference CSV file

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