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Old 06-21-2011, 06:37 PM   #3
Junior Member
Location: Boston

Join Date: Feb 2011
Posts: 3

Hi mudshark,

I am not entirely sure about all aligner parameters since I have only received aligned reads from our seq facility. I would have to ask them for more details if this turns out to be the crucial point. This is as much as I know: they use the first 25nt of a read as a seed and allow 2 mismatches. If multiple matches for a seed are reported, quality scores for the entire read are taken into account and the read will be called as 'multiple' or 'unique' based on parameters that I am not aware of.
Multiple matches and duplicates were excluded in the analysis.
I have not yet done qPCR on the library.

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