Identification of non-coding RNAs from RNASeq data

[zee]

I am interested in finding noncoding RNAs, particularly small RNAs from Illumina or SOLiD sequencing data prepared with RNASeq protocol.
Apart from intersecting my mapped reads with mirBASE or other annotated small RNAs, what could I use for detecting noncoding RNAs from from RNASeq data?
I know that we could just do a small RNA prep but I'm sure there are people who have attempted this sort of approach before to maximize what they get out of their RNASeq.

[NicoBxl]

miRDeep or miRTrap are good programs

1. Map your reads to a reference genome (discard the reads who not )
2. Map your reads to the miR from mirbase ( be aware of the isomirs )
3. With the rest of your reads, use miRDeep or miRTrap