Entering edit mode
13.8 years ago
Paul
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760
If a read has a zero quality score in MAQ does that mean:
a) The read aligns to multiple positions b) The read aligns to nowhere
I think it's either one or both of these but I'd hope someone can clear it up for me?
Well they could be from paralagous genes or repetitive sequences. It's kind of hard to just make a general rule on non-specific matches. Have a read of this: http://www.nature.com/nmeth/journal/v5/n7/full/nmeth.1226.html
Oh right, dunno how I missed that, is there really any point in filtering these out if this is the case? I'm analyzing some rna-seq data.