I'm looking for tools to semi-automate finding non-coding RNAs in bacterial RNA-seq data. I've been able to find some tools but I'm still quite lost (see link below).

I've also seen this Biostar post (http://www.biostars.org/p/1662/).

The few papers I could find don't follow a common method.

Can anyone recommend me the best approach?

Thanks, Bernardo

P.S. Some more tools: http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Software%22%5BMesh%5D+AND+non-coding+RNA

http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Software%22%5BMesh%5D%20AND%20ncRNA%20RNAseq