I am working on a transcriptome project where I have ~400MB-in-length 454 mRNA-seq reads sequenced on a non-normalized cDNA library. I was using mira3 to do de novo assembly of my reads, and it produced a decent assembly over transcripts with a moderate expression level. However, mira has a hard time assembling those highly expressed transcripts (>1000 copies or more). And it's the same thing with cap3. The TIGR assemler (TGICL) offers some ways to deal with highly expressed transcripts, but it doesn't have a great answer either.
I wonder if anyone has insight of assembling high-expression transcripts? Could de bruijin graph-based assemblers work in this scenario?
Many thanks,
Hao
I wonder if anyone has insight of assembling high-expression transcripts? Could de bruijin graph-based assemblers work in this scenario?
Many thanks,
Hao
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