I have some long reads sequencing data of Oxford nanopore technology. I mapped reads to the human genome via minimap2, mapping makes sense but as expected, there are many seq errors and gap openings. Now I want to have read count per gene. For this end I tried to run Salmon, using an indexed human transcriptome, but most of the reads were filtered out due to low alignment score.
What is the best practice for RNA-seq quantification of long read data?
thanks a lot! Gat.