Cufflinks and class codes

Question

[int11ap1]

Hello to everybody,

what do you think, class "o" transcripts should be described as novel isoforms or as a new locus?

Thanks.

Answer 1

[Sukhi Singh]

I can't answer your question exactly, but quite some info here: http://seqanswers.com/forums/showthread.php?t=3518

The 'o' code stands for "other overlap" - that is an exonic overlap with the reference transcript that doesn't fall in any other, "more interesting" overlap categories - e.g. no splice sites match ('j' class), no containment ('c' code) etc. These 'o' codes could be assigned, for example, to assembled single-exon fragments that happen to overlap one of the terminal exons of a reference transcript (but not enough to make it "contained").