> For the complete documentation index, see [llms.txt](https://help.connected.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.connected.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                                          |
| \<Sample\_ID>.scRNA.singlet\_cell\_guide\_assignments.csv  | CSV containing only cells for which exactly one guide RNA feature was called                                                              |
| \<Sample\_ID>.scRNA.guide\_metrics.csv                     | CSV metrics file containing guide calling metrics                                                                                         |


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