Detect cleavage sites in bacterial RNAseq data

Question

[pravee1216]

Dear Folks -
Do you know any (published) bioinformatics protocol for detecting the cleavage sites in RNA using whole transcriptome (RNAseq) data of bacteria? The total RNA of bacteria has been treated with Ribo-Zero rRNA kit before sequencing on Illumina HiSeq platform. Looking forward a right methodology for identifying genes that are cleaved at specific sites in case samples. Please suggest your views
Thanks
Raj