Cell Ranger6.1, printed on 11/21/2024
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.