Minimap2 giving opposite strand orientation than Pychopper

Question

[vanda.gaonach-lovejoy]

Hello! We sequenced cDNA using nanopore technology. I used Pychopper to orient my reads before mapping them to the human reference genome. However, when after the reads are mapped, many of them are the opposite orientation as predicted by pychopper. Why could that be? Thank you!

[muhammad_elhossary]

I have the same issue, could you know why?

[biofalconch]

What's the proportion of reads mapping in the opposite orientation?