Table 2.

Comparison of Tiling Assembly to Cufflinks

Category	Tiling Assembly	Cufflinks
Novel gene findinga	3,473 genes	52 genes
False-positive rateb	17 out of 100 genes	25 out of 100 genes
Ease of use	User interface	Command line
Algorithm	Read tiling	Bipartite graph
Minimum expression	100 RPKE	100 RPKE
Run timec	3–4 h	1.5 h
Transcripts identified	Single transcript	Multiple transcripts

^aThese figures represent genes found exclusively by either TA or Cufflinks that have an expression level greater than 100 RPKE, prior to percent similarity filter.

^bData from random genome with 100 known genes inserted. No filtering performed.

^cExcludes set-up time. Set-up for Tiling Assembly and Cufflinks is about the same time.