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transcript assembly and full length

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
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written by qudrat qudrat

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

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written by vinayjrao vinayjrao

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

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written by vinayjrao vinayjrao

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.

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written by qudrat qudrat

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