read count for RNA sequencing via nanopore

Question

[gat]

Hi all,

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.

[GenoMax]

Have you checked the pipeline provided by ONT?

[colindaven]

GenoMax makes a good suggestion. Generally the next step would be use of a tool like FeatureCounts or htseq-count to get the read counts.

AFAIK Salmon is a kmer tool intended for short reads, so not applicable here.