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Old 05-07-2010, 06:40 AM   #1
Location: NJ

Join Date: Mar 2010
Posts: 18
Default cufflinks and non-uniquely mapped reads

Cufflinks appear to take not only uniquely mapped reads. I only filtered out low quality mapped reads and ran cufflinks without any problem. But how cufflinks take care of those reads mapped to multiple regions? Does it only pick the region with highest mapping score? Anyone has ideas?

I am wondering how the results will differ if I use uniquely mapped reads only.

Any input will be highly appreciated.
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