11 the rst step is to idenefy pairs of incompaeble

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Unformatted text preview: NA fragment sequences that have been aligned to the genome by using so^ware that is capable of doing split alignments (i.e. TopHat). •  With paired ­end RNA ­seq, Cufflinks treats each pair of fragment reads as a single alignment. The algorithm assembles overlapping “bundles” of fragment alignments separately. – This reduces running Eme and memory usage. 11 The first step is to idenEfy pairs of incompaEble fragments that must have originated from disEnct spliced mRNA isoforms. Fragments are connected in an “overlap graph” when they are compaEble and their alignments overlap in the genome. Each fragment has one node in the graph, and an edge, directed from le^ to right along the genome, is placed between each pair of compa>ble fragments. 12 13 Isoforms are then assembled from the overlap graph. Paths through the graph correspond to mutually compa>ble fragments that could be merged into comp...
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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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