transcript assembly and full length

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6.5 years ago

qudrat ▴ 100

Hello folks! I have a transcript which is partial in length (obtained by TopHat/Cufflinks analysis) and I want to get its full length. Is there any way to get a full length transcript? Please suggest any Bioinformatics method.

RNA-Seq alignment • 1.3k views

ADD COMMENT • link 6.5 years ago by qudrat ▴ 100

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Hi, could you please elaborate your issue, or maybe paste the partial sequences obtained?

ADD REPLY • link 6.5 years ago by vinayjrao ▴ 250

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blast it.

ADD REPLY • link 6.5 years ago by cpad0112 21k

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That could be done, but I was wondering if partial transcripts are generally obtained?

ADD REPLY • link 6.5 years ago by vinayjrao ▴ 250

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Actually Cufflinks assemble sequences parsimoniously so there is a chance to get partial sequence. The sequence I have got does not show any feature of 3'UTR. One more thing is that I have got a peptide sequence that map to chromosome 1 but my transcript is short of 100 bp. (peptide map 100 bp upstream of transcript first base). I have read many papers that have talked about partial assembly of transcript sequence.

ADD REPLY • link 6.5 years ago by qudrat ▴ 100

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