Automated transcription definition improvement. (A) Graphical representation of Partek® Genomics Suite™ improvement. Partek found regions that had reads in places that Cufflinks could not define transcripts. Regions with a minimum coverage of 50 reads and a length of at least 300 bp were selected for defining further transcripts. (B) Clustering of the transcripts found by the four methods (CLC Assembly Cell, Cufflinks and Cuffcompare, ESTs and Partek) using two different tools (TGICL, CAP3) and combining the results of both. tx = transcripts. (C) Venn diagram of the “gold standard” genes found in each of the four approaches.