I am looking at some PAR-clip data. trimming and mapping went perfectly, however, when i look at the data on IGV, in the plus strand i have a vast majority of T to C mutations (as expected), but in the minus strand i see a lot of T to G mutations, like a vast predominance.
is there any way to explain this? how is it possible that only the minus mapping reads are affected? there must be a technical issue somewhere!