Cufflinks and Scripture: Two New 'Splice-Aware' Tools for the RNA-Seq Analysis Pipeline

Cufflinks and Scripture both take an "align-then-assemble" approach, which first relies on "splice-aware alignment" of the RNA-seq reads to the genome, and then reconstructs transcripts from the spliced alignments. Both tools use TopHat, developed at the University of Maryland, for the alignment step.

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