STAR-long parameters for aligning RNA ONT reads to genome
I've had great results using minimap2, particularly when combined with a pre-treatment of Canu for error correction (using minimap2 for the read-to-read mapping):

# correct reads
~/install/canu/canu-1.6/Linux-amd64/bin/canu overlapper=minimap \
   genomeSize=100M minReadLength=100 minOverlapLength=30 -correct \
   -p 4T1_BC06 -d 4T1_BC06 \
   -nanopore-raw workspace/pass/barcode06/fastq_runid_*.fastq
# align reads
~/install/minimap2/minimap2 -p 10 \
   -a ~/db/fasta/mmus/ucsc/mmus_ucsc_all_cdna.idx \
   -x splice &lt;(pv all/4T1_BC06/4T1_BC06.correctedReads.fasta.gz) | \
  samtools sort &gt; 4T1_BC06_all_vs_mmusAll.bam


Update: the most recent nanopore basecaller, combined with the most recent minimap2, seems to now do a decent job with mapping, and pre-correction of reads no longer seems necessary. More recently I've been using LAST to map to the transcriptome, and minimap2 to map to the genome. Minimap2 has the ability to use a homopolymer-compressed genome index, which means that the most common consistent error for nanopore reads (i.e. misjudgement of homopolymer length) will not influence the mapping rate.