Gene Expression Quantification

The DRAGEN RNA pipeline contains a gene expression quantification module that estimates the expression of each transcript and gene in an RNA data set. The module first internally translates the genomic mapping of each read (read pair) to the corresponding transcript mappings. Then uses an Expectation-Maximization (EM) algorithm to infer the transcript expression values that best match all the observed reads. The EM algorithm can also model and correct for GC-bias in the reported quantification results.

To enable the quantification module, set the --enable-rna-quantification option to true in your current RNA-seq command-line scripts. Additionally, you must provide a gene annotation file (GTF/GFF) that contains the genomic position of all transcripts to quantify. You can specify the GTF/GFF file using the -a or --annotation-file option.