Qualimap result interpretation

Question

[Aura]

Hi there. Newbie here. I have got my Qualimap results summary for my alignment from SOLiD genomic reads to a reference genome; yet I can't easily decide if the alignment was good enough. I know it wasn't optimal, but was it really bad? Bad enough to discard?

For example, which 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 alignment is good enough for further analysis?

Thanks for all the help.

Answer 1

[Antonio R. Franco]

Maybe that 50 is not too bad.

Take a look to this http://seqanswers.com/forums/showthread.php?t=3142

I think however, that the quality mapping values should be more clearly described

[Aura]

Certainly, they should be more clear. Yet, If I understood it well, being my quality mapping value over 3 it should be OK. Well, I guess that I'll keep my alignment. Thank you, Antonio.