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  • PAR-clip T to C mutations become T to G in the minus strand in IGV?

    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, does anyone have any idea?

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