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Old 02-05-2010, 10:05 AM   #2
Senior Member
Location: Kansas City

Join Date: Mar 2008
Posts: 197

Cufflinks will give you a gene/transcript and its RPKM (if you feed it a gff file). If you don't, it will give you a "made up" gene/transcript and its RPKM.

RPKM is always in terms of a larger genomic entity, not a single read. Reads per kilobase per million.

Hi, fellow Kansas Citian!
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