I'm looking for transcripts in an poorly annotated retrovirus, using oxfort nanopore reads. Currently, I'm trying to first "correct" the trimmend read sequences with the software
canu and plan to do the assembly using the
PASA pipeline (which uses the
I'm completly new to long read processing and wanted to ask, if there are maybe better workflows for that purpose, or if there is an alternative. I also tried
stringtie, but I only got transcripts which were one exon long.