Use cDNA to polish exons

[SalvadorGJ]

Hi!

I have long cDNA reads which I want to use as input for genome polishing, expecting that they will only fix exons across the draft reference. Have you tested racon with cDNA alignments before?

I was wondering about how racon deals with "N" operators (CIGAR) of SAM/PAF alignments, as these are suggested to represent introns on mRNA-to-genome alignment. With this in knowledge, do you think it is capable to differentiate between real introns (which are not intended to be removed) and insertions on draft's exons (which should be polished)?