Are there any suggested parameters to align ONT reads to the reference genome using STAR-long? For now, I used the parameters suggested here, but I noticed a weird behaviour.
I have RNA reads (D. melanogaster) from
R9 flowcells, separately. I only selected to analyze
2D reads in
I have, respectively, 113249 reads for
R7 and 40318 reads for
R9. I aligned those reads and get (only!) 150 uniquely mapped reads for
R7 data and 8017 uniquely mapped reads for
R9 data. I tried to run again the same command on a different server with fresh compilation, but the output file is consistent with these 150 reads.
However, if I align the same with GMAP, I get 78016 uniquely mapped reads for
R7 and 33523 uniquely mapped reads for
R9, so I suspect that something went wrong in the alignment run.
I am aware that the two mappers behave very differently, STAR-long being more precise and preferring to report mappings of fewer reads but at better loci, and GMAP being overall less precise, trying to map the most of the reads but at not-so-good loci.
I was wondering if some of you had experience with this and could suggest me the best parameters for RNA reads from ONT?