Hi there. Newbie here. I have got my Qualimap results summary for my aligment from SOLiD genomic reads to a reference genome; yet I can't easily decide if the aligment was good enough. I know it wasn't optimal, but was it really bad? Bad enough to discard?
For example, wich is the minimum acceptable value of mapping quality across the reference? Mine is around 90, with some terrible points with value of 50.
Which other parameters should I check in order to decide if this aligment is good enough for futher analisis?
Thanks for all the help.