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