Orientation of reads are the opposite of what is expected

[Prakrithi-P]

Hi, Thanks for the great tool. I have been using scNanoGPS but looks like all reads that are expected to map to + strand are assigned with minus and the other way around. I am not sure why this is happening. I did several sanity checks of the reads as well but still looks like the strand assignment is the opposite. Could you please help me with this?

Thanks and regards, Prakrithi