Rna-Seq With Reference Genome But No Gene Annotations

Question

[Honey]

I have an RNAseq data from a fungi and the public database for that particular fungi has whole genome shotgun sequences. But there are no gene annotations. Is it possible to analyze RNAseq data for differential expression by aligning to the shotgun reference genome.

Thanks

Answer 1

[Fabio Marroni]

Yes, for example you can use cufflinks to assemble trnascript without genome annotation: read the documentation here http://cufflinks.cbcb.umd.edu/

Answer 2

[Nicolas Rosewick]

On idea is to use a well annotated related species (in your case another fungi ) and to map the gene sequences ( use cDNA sequences, so UTR+exons ) with gmap ( it can output a gff file) to have an basic annotation.