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Old 06-03-2010, 09:53 AM   #1
Location: IL

Join Date: May 2010
Posts: 10
Default Maq mapping score and "Mapping uniquely"??

When Maq is used for RNA-seq data analysis, I saw several people set (q) "Minimum mapping quality allowed for a read to be use" to be 30 as the cutoff value in %Maq pileup. Does this mean the reads after this "pileup" with q=30 are those "mapped uniquely"?

But, since "most of the repetitive reads have a mapping score of 0", why just set the q to be a value a little bit > 0 (other than 30) to discard the non-unique reads? Or in another word, what value should we set for q such that we can confidently say that we have filtered out all the non-unique mappings?


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