Looking for tools to find non-coding RNAs in bacterial RNA-seq data

[bernardo_bello]

Hi,

I'm looking for tools to semi-automate finding non-coding RNAs in bacterial RNA-seq data. I've been able to find these or these tools, but I'm still quite lost. I've also seen this Biostar post.

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

Can anyone recommend me the best approach?

Thanks, Bernardo

P.S. I posted the same question in Biostar forum.

[TiborNagy]

I have read an article about non coding RNA classification using trinucleotide distributions. I will link it here.

[Leandrofm]

I used RNA-seq.
Firstly I masked the ORFs and then aligned the RNA-seq reads to the masked genome. Cufflinks was very useful for doing the annotation.

L.-

[bernardo_bello]

I used RNA-seq.
Firstly I masked the ORFs and then aligned the RNA-seq reads to the masked genome. Cufflinks was very useful for doing the annotation.

L.-

Could you share you commands? Thanks!