I am looking for suggestions on how to assemble a single, fairly complex transcript sequence from RNA-Seq data. The protein this transcript encodes has a variable number of repeated 10 a.a. domains. Assembling with Trinity or SOAPdenove-trans did not generate a complete sequence for the proteins -- the protein does not other domains found in known orthologs.
I also tried aligning reads against orthologs (used usearch) and I assembled those reads that aligned using CAP3 and Velvet. That approach did actually worse than Trinity.
Any suggestion on how to accurately assemble that single sequence?