Hello,
I am using Polyester for simulating RNA-seq data based on a counts matrix which I have created from real data. Therefore, I use the simulateexperimentcountmat function, with a gtf file and chromosome fasta files:

simulate_experiment_countmat(gtf = "...", seqpath = "...", readmat = counts_matrix, outdir = "...")

However, I am unclear about how to make the order of genes in the counts matrix match the gtf. My results seem to be mixing the gene order, so assigned counts are applied to the wrong gene.
Had anyone ever tried this and can tell me how the problem may be addressed?
Thanks!