Gene Annotation Input Files

When processing RNA-Seq data, you can supply a gene annotations file by using the --annotation-file option. Providing this file improves the accuracy of the mapping and aligning stage (see Input Files). The file should conform to the GTF/GFF format specification and should list annotated transcripts that match the reference genome being mapped against. The similar GFF3 format is currently not supported.

DRAGEN can take the SJ.out.tab file (see SJ.out.tab) as an annotations file to help guide the aligner in a two-pass mode of operation.