I have quant.sf files generated by Salmon by mapping 100bp single-end Illumina libraries against primary transcripts. The genome for this species is not so perfect and is missing some genes of interest. So I am using both transcriptome and genome data for this RNA-seq.
Before passing this quantification data, I needed to run Tximport and generated a table containing transcript ID and gene ID from a gff3 file based on the genome annotation. Then, I realized many of the primary transcripts were missing in the genome.
I was going to add the unique transcript ID and some arbitrary gene ID into the table. But is this okay? What would be the standard protocol to deal with this?