Transcript assembly in very dense genomes

[Vanda]

Dear all,
I have performed RNASeq on Illumina Ga2x of a virus with a very dense genome (most genes are overlapping each other). I have tried using Cufflinks on Galaxy however the results I have got obviously implicate that the program is havnig problems with dense genome (this virus has over 200 genes, RNASeq was done on a permissive cell line so most of the genes are expressed - cufflinks predicted only 7 genes!!!).

Now, I used cufflinks on ELAND alignment so I'll rerun it first through TopHat however in the mean time maybe someone has already en****ere such problem?

Thanks!

[dsher]

Hello,
I saw you posted this thread some time ago... did you get any answers, or have you solved the problem? We have a similar case with a high-density bacterial genome, where overlapping genes get "FPKM=0".
Thanks
Daniel