How to predict gene structure from RNA-seq data?

[LaurentV]

Hi all,

I have RNA-seq data that I would like to use to predict gene structures in mapping them on a reference genome.

FYI, I started from Illumina (75bp) and 454 single read RNA-seq data. I was able to map RNA-seq data by simply blasting RNA-seq sequences on the genomic location of interest. The mapping results allow to identify the structure of the gene (exons & introns boundaries) but I now need a tool to merge them all in one CDS sequence (from ATG to STOP codon).

I tried several tools such as Splign, EST2Genome, but they all give individual gene structures from every individual RNA-seq read. They don't merge them all in one complete gene structure.

Does anyone have an idea on how to proceed? Do you know any tool/software being able to automatically "predict" gene structure using a reference genome and expression sequence data (EST, RNA-seq, etc)?

Thanks in advance for your help!
Laurent

[blue mood]

If you have a reference genome, i would advise you to use tophat and cufflinks. The alignment sam/bam of tophat can be assembled into transcripts by cufflinks.