This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Cufflinks Transcript Assembly

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!

cufflinks transcript assembly
• 4,576 views • link
updated by Wen.Huang Wen.Huang • written by Stevelor Stevelor

Did you define the library type in your cufflinks run?

• 0 views • link
written by Damian Kao Damian Kao

1 answer

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

• 0 views • link
written by Wen.Huang Wen.Huang

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

• 0 views • link
written by Stevelor 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 :(

• 0 views • link
written by Stevelor Stevelor

Log in to answer this question.

More posts like this