> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/dragen-single-cell-rna/analysis-results/secondary-analysis-results.md).

# Secondary Analysis Results

The following table describes the files created by DRAGEN Single Cell RNA:

| File                                                          | Description                                                                                                                                                 |
| ------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------- |
| \<Sample\_ID>.scRNA.bam                                       | Binary Alignment Map (BAM) files containing information about all reads in the input FASTQ files that were mapped to the reference genome                   |
| \<Sample\_ID>.scRNA.bam.bai                                   | Index file for the BAM for use by downstream applications                                                                                                   |
| \<Sample\_ID>.scRNA.barcodeCounts.txt                         | Text file containing the counts per barcode                                                                                                                 |
| \<Sample\_ID>.scRNA.barcodeSummary.tsv                        | Summary of barcode statistics including number of reads, genes, and molecules in each barcode                                                               |
| \<Sample\_ID>.scRNA\_metrics.csv                              | Single cell metrics summary with assay sensitivity and quality metrics                                                                                      |
| \<Sample\_ID>.scRNA.moleculeInfo.h5                           | Summary of the read counts for each barcode, gene, BI, and IMI combination in HDF5 format.                                                                  |
| \<Sample\_ID>.scRNA.matrix.mtx.gz                             | Sparse matrix with rows that represent genes and features detected, and columns that consist of all barcodes that were detected                             |
| \<Sample\_ID>.scRNA.features.tsv.gz                           | Information about the features corresponding to the rows of the sparse matrix                                                                               |
| \<Sample\_ID>.scRNA.barcodes.tsv.gz                           | List of barcodes corresponding to the columns of the sparse matrix                                                                                          |
| \<Sample\_ID>.scRNA.h5ad                                      | Count matrix in AnnData format. Barcodes are stored in the OBS group and genes are stored in the VAR group.                                                 |
| \<Sample\_ID>.scRNA.filtered.matrix.mtx.gz                    | Filtered sparse matrix with rows that represent genes and features detected, and columns that consist of all barcodes that were detected                    |
| \<Sample\_ID>.scRNA.filtered.features.tsv.gz                  | Information about the features corresponding to the rows of the filtered sparse matrix                                                                      |
| \<Sample\_ID>.scRNA.filtered.barcodes.tsv.gz                  | List of barcodes corresponding to the columns of the filtered sparse matrix                                                                                 |
| \<Sample\_ID>.scRNA.filtered.h5ad                             | Filtered count matrix in AnnData format. Barcodes are stored in the OBS group and genes are stored in the VAR group.                                        |
| \<Sample\_ID>.scRNA.positive\_cell\_guide\_assignments.csv    | CSV containing all passing cells with information on guide RNA sequences called for each barcode. Only output when guide calling is enabled.                |
| \<Sample\_ID>.scRNA.singlet\_cell\_guide\_assignments.csv     | CSV containing only cells for which exactly one guide RNA feature was called. Only output when guide calling is enabled.                                    |
| \<Sample\_ID>.scRNA.simple\_threshold\_guide\_assignments.csv | CSV containing all cells containing more gRNA counts than a set threshold (default 10). Only output when guide calling is enabled.                          |
| \<Sample\_ID>.scRNA.guide\_metrics.csv                        | CSV metrics file containing guide calling metrics. Only output when guide calling is enabled.                                                               |
| \<Sample\_ID>.scRNA.feature\_barcode\_reference.csv           | A copy of the feature barcode reference CSV provided when feature counting is enabled                                                                       |
| \<Sample\_ID>.scRNA.direct\_capture\_barcode\_reference.csv   | A copy of the direct capture barcode reference CSV provided to DRAGEN when direct capture mode is enabled                                                   |
| \<Sample\_ID>.scRNA.read\_group\_metrics.csv                  | Single cell metrics on a per-read group basis (for each RGID provided to DRAGEN)                                                                            |
| \<Sample\_ID>.scRNA.feature\_type\_metrics.csv                | Single cell metrics for each feature type based on types in the feature barcode reference provided to DRAGEN. Only output when feature counting is enabled. |


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