overlapping transcripts? --jaccard_clip with Trinity

[johnsolk]

Are transcripts overlapping?
http://pasapipeline.github.io/

Note
When applying Trinity to RNA-Seq samples derived from microbial eukaryotes, using either genome-free or genome-guided de novo assembly, be sure to use the --jaccard_clip parameter to reduce the occurrence of falsely-fused genome-neighboring transcripts. Also, only include Cufflinks transcripts if applying the approach to expansive genomes of animals such as mouse or human, and exclude Cufflinks from application to compact microbial eukaryotic genomes.