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Old 11-03-2016, 06:28 PM   #3
Junior Member
Location: Boston Ma

Join Date: Oct 2016
Posts: 1
Default My experience with cufflinks

Cufflinks will use the mapped reads and the reference genome to create a parsimonious assembly (a minimum spanning tree-esque structure) that explains the reads. The logic of the algorithm is based on the Burset and Guigo paper (Burset, Guigo, Evaluation of Gene Structure Prediction, 1996) and their observations regarding high false positive rates of gene finding programs that are guided by annotation. This is my understanding of the matter based on the past year I have spent working on similar issues.
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