Target prediction between complementary RNA-seq and Small-RNA-seq data sets

[Amielynn]

Hi everyone-

Short background: I have Illumina sequence data on mRNA and microRNA from the same samples. Theoretically these two separate lists of sequences should contain complimentary microRNAs and mRNAs. I have no reference genome for my species however many of my microRNAs match to already annotated sequences from related species on miRBase along with a few potential novel microRNAs.

Question: Does anyone know if it is possible to datamine these two profiles and predict mRNA-microRNA targets from de novo assembled transcriptome data? There seem to be many programs that utilize reference transcriptome data but I am not interested in that since I have assembled the transcriptome for my species de novo from the mRNA RNA-seq data.

I'm not sure if I can use de novo assembled transcriptome data for microRNA target prediction through already existing programs; I currently have a subscription to CLC genomics workbench which appears unable to do so. This could potentially require the development of a custom script... Any information would help!

Thanks!

arom2