Hello,

I'm working with ONT RNA seq data and I used the cDNA direct seq to do the seq. I want to look for long deletions in mRNAs that are not spliced, for this, I want to use the splice option of minimap2 with the following options:

minimap2 -ax splice -un -k 14 --splice-flank=no -x map-ont Reference.genome.fasta Input.fastq > Output.sam

(1) For the RNA direct seq I found that many people use the -k 14 option nevertheless, considering that the cDNA seq is also noisy I wonder if I should use it as well.

(2) Not sure if --splice-flank=no will have an effect after the -un option.

(3) Almost the same question, not sure if -x map-ont will have an effect.

If there are better options that I should use please let me know.

Thanks! Francisco