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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?

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  • $\begingroup$ Another way to look at this question is that. What's the precise definition that two transcripts are considered equal and thus my experiment has positively assembled the transcript. $\endgroup$
    – SmallChess
    Jul 22, 2015 at 8:57

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If some exons are missing in one of the samples then the introns will, by definition, be different. What this allows is for the bounds of the outermost exons to vary a bit. This is particularly useful for exon 1, which often has lower coverage.

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  • $\begingroup$ Thanks for the reply. However, I'm still not very sure how two transcripts are compared as stated in the paper. In this context, what's the precise definition of a match? Does that mean if I have 10 exons in the reference, and I get 8 of those exons (excluding the first and last exon), it's a match? $\endgroup$
    – SmallChess
    Jul 22, 2015 at 8:56
  • $\begingroup$ Forget about exons, you can clearly see that what you posted doesn't mention them. $\endgroup$
    – Devon Ryan
    Jul 22, 2015 at 9:06
  • $\begingroup$ Yeah, that's my question. What do they really mean in the paper? I tried to digest it but I couldn't understand what they meant. $\endgroup$
    – SmallChess
    Jul 22, 2015 at 9:09
  • $\begingroup$ Draw out a few example isoforms on a piece of paper. Have one skip an exon. Are the introns then the same between them (no). What if the exons are the same except the TSS or TES differs a little, are the introns then the same (yes). $\endgroup$
    – Devon Ryan
    Jul 22, 2015 at 9:15

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