In this paper, the cuffcompare RNA package is reported:
Because of the stochastic nature of sequencing, assembly of the same transcript in two different samples may result in transfrags of slightly different lengths. A Cufflinks transfrag was considered a complete match when there was a transcript with an identical chain of introns in the combined annotation.
What does this mean in terms of comparing two transcripts to see if they are the same? Does that mean two transcripts are considered equal if they have the same introns, even some exons are missing in one of the transcript? What do they mean by transfrag? Is there an example?