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Old 04-06-2010, 05:46 AM   #19
RockChalkJayhawk
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Location: Rochester, MN

Join Date: Mar 2009
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To answer your question, see this page <a href="http://cufflinks.cbcb.umd.edu/howitworks.html"> here</a>
Quote:
To estimate isoform-level abundances, one must assign fragments to individual transcripts, which may be difficult because a read may align to multiple isoforms of the same gene. Cufflinks uses a statistical model of paired-end sequencing experiments to derive a likelihood for the abundances of a set of transcripts given a set of fragments.
Therefore, cufflinks is using probabilities to assign individual fragments to individual transcripts. Since the units of the counts are in fragments per KB transcript per million reads, you can convert them back to raw integers by the multiplying the length of a given transcript and number of reads in millions.
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