Bacteria intergenic regions RNA-seq

[honey]

If I am specifically interested in differential expression of intergenic regions in bacterial RNA-seq. Do I need to have riodepleted/ ribo zero libraries or polA should work fine?

Thanks

[Jean]

Well, poly-A enrichment for bacterial RNA will not work because the RNA molecules are not typically poly-adenylated unless for degradation. You will have to do some kind of mRNA enrichment/rRNA depletion otherwise there will be excessive rRNA molecules sequenced and not much else.