To get a transcript counts matrix, we recommend finding a compatible short-read dataset (in case you did not generate Illumina data for your samples) and map these Illumina reads to your species' genome using the curated GTF from SQANTI3. To get transcript counts fast, you can use a pseudoaligner such as Kallisto, or use a splice-awer mapper such as STAR followed by a quantification tool like RSEM to get counts.