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Old 09-17-2010, 08:41 AM   #1
Location: Institute, WV

Join Date: May 2010
Posts: 24
Default Regarding Unique reads, Unique alignments

I have few questions regarding the best practices that are adopted, in dealing with multiple alignments from a single read and presence of identical reads in the data (from Biology stand point for the later meaningful analysis of data) :

I am curious, how important it is to deal with identical reads.
Having many identical reads in data means something wrong with the

What could be considered as max. cutoff value for the number of identical reads in the data, so as to not consider those reads?

In the other case of a single read aligning at multiple places in a genome, what should be the cutoff value for number of multiple alignments, so as to not consider those reads?
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