Cuffcompare. Differences between class codes "=" and "i"

Question

[Antonio R. Franco]

According THIS DOCUMENT, after nunning cufflinks/cuffcompare to reconstruct the transcripts with a gtf reference genome

Class code "=" is a Complete match of intron chain

Class code "i" is a transfrag falling entirely within a reference intron

Can anybody tell the difference?

Answer 1

[andrew.j.skelton73]

So a "transfrag" refers to your TCON IDs, and it's the transcript identified by Cufflinks. This means that a class code of "i" denotes the TCON falls completely within a intron from the reference annotation you provided, that suggests to me that there's at least 2 exons that completely match to annotation.

Class code "=" suggests that the TCON is a complete match of all the introns in the reference transcript, meaning that it's in theory a complete match of the reference transcript. The issue with the lack of these definitions means that it's open to interpretation, but I've always assumed that that "=" is a complete reference transcript match with the caveat that it's ignorant to the 5' first exon and 3' last exon.