I have just done a set of nanopore sequencing with PCR based cDNAseq. Any suggestion for analysis? Can minimap2 do this job. I have the genomic assembly/interested contigs.
Yes, Minimap2 can map nanopore reads to a custom reference.
Our tutorials are here: Galaxy Training!
Not all tools wrapped in Galaxy have a dedicated tutorial, but each tool has help directly on the form plus link outs to the author resources, publications, possibly more tutorials, etc.
What is your goal?