Splice Junction Mapper For Dense Genome

Question

[Nicolas Rosewick]

Hi,

Is there a splice junction mapper for RNA-Seq reads for dense genome (like viruses) ? Or maybe use an more general tool (tophat, splicemap,...) with specific parameters ?

Thanks,

N.

[Sean Davis]

Do you know the transcript structures for this genome? If not, do you know what splicing signals are used?

[Nicolas Rosewick]

I mean that there are a lot of overlapping transcript