RNAseq in bacteria-phage system

[fcarrasco]

Hi, we are going to perform RNAseq in a bacteria-phage system. Our bioanalyzer profiles show a huge proportion of what we think must be small RNAs (around 26 seconds in the X axis) with respect to the typical 23 and 16S ribosomal peaks (40 and 45 seconds). We are worried that after ribosomal RNA depletion most of our RNA might be small RNAs instead of mRNAs. Did anyone experienced this kid of profiles? If so, did you go ahead and succeeded in the RNAseq?

By the way, the small RNA fraction comes from bacteria since it is also present in the uninfected controls.

Thank you!

Fernando