Cufflinks Transcript Assembly

Question

[Stevelor]

Hi,

does anyone of you know how cufflinks defines the direction of the assembled transcripts?? We used illumina 50bp unstranded SE reads...the result looks strange in some cases....so for example there are some antisense-transcripts or transcripts which overlap. Didn't find anything about that in the manual!

Thanks!

[Damian Kao]

Did you define the library type in your cufflinks run?

Answer 1

[Wen.Huang]

I think for multi-exonic transcripts, they used the splice sites to determine the strand when the library is unstranded.

[Gireesh K. Bogu]

how about single exon transcripts ?

[Stevelor]

yes of course...so i am wondering that cufflinks doesn't give an output e.g. with all transcripts in one direction...

[Stevelor]

That's what i also thougt cause it's the only possibilty for giving an direction....i am goign to check if all these antisense transcripts have more than one exon....but then we still don't know about single exon transcripts :(