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. Author manuscript; available in PMC: 2013 Mar 1.
Published in final edited form as: Nat Protoc. 2012 Mar 1;7(3):562–578. doi: 10.1038/nprot.2012.016

Figure 3.

Figure 3

Merging sample assemblies with a reference transcriptome annotation. Genes with low expression may receive insufficient sequencing depth to permit full reconstruction in each replicate. However, merging the replicate assemblies with Cuffmerge often recovers the complete gene. Newly discovered isoforms are also integrated with known ones at this stage into more complete gene models.