Extends the work of tophat pachter lab the rna

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Unformatted text preview: de assembly 5 Reference Guided Transcript Assembly Cufflinks (Trapnell et al) •  Cufflinks: an algorithm that idenEfies complete novel transcripts and probabilisEcally assigns reads to isoforms. •  Extends the work of TopHat (Pachter lab). •  The RNA sequence fragments are mapped to the reference using TopHat. •  Aim is to recover the minimal set of transcripts supported by the alignments. 7 8 Cufflinks (Trapnell et al) •  A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. •  Uses a comparaEve transcriptome assembly algorithm to produce the minimal set of transcripts supported by the fragment alignment. •  Reduces the transcript assembly problem to finding a maximum matching in a weighted bipar>te graph. 9 TopHat CuffLinks 10 Cufflinks (Trapnell et al) •  Takes as input cD...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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