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Old 10-11-2010, 04:37 PM   #1
frankyue50
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Default should RNA-seq use monoclonal reads

hi, guys, I was wondering what's your take on this. Tophat will accept reads that are mapped up to 20 locations and take a fraction for each location. Well, this could be helpful to identify homologous genes, but also create a lots artifact. Do you think we should stay with reads that mapped only once in the genome?
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Old 10-12-2010, 01:17 AM   #2
kopi-o
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That's not "monoclonal" reads, but rather "multi-mapping" reads.

Personally I think it is too restrictive to require unique mappings in RNA-seq. It's a matter of taste as well as organism + application.
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