Question

Cufflinks Transcript Assembly

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12.7 years ago

Stevelor ▴ 310

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 • 3.8k views

ADD COMMENT • link updated 12.7 years ago by Wen.Huang ★ 1.2k • written 12.7 years ago by Stevelor ▴ 310

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Did you define the library type in your cufflinks run?

ADD REPLY • link 12.7 years ago by Damian Kao 16k

score 3 · Answer 1 · 2012-03-08

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12.7 years ago

Wen.Huang ★ 1.2k

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

ADD COMMENT • link 12.7 years ago by Wen.Huang ★ 1.2k

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how about single exon transcripts ?

ADD REPLY • link 12.7 years ago by Gireesh K. Bogu ▴ 100

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

ADD REPLY • link 12.7 years ago by Stevelor ▴ 310

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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 :(

ADD REPLY • link 12.7 years ago by Stevelor ▴ 310