Bacteria Intergenic Regions Rna Depleted

Question

[kanwarjag]

I was wondering if I need to get the data (differential expression) in the intergenic regions of bacteria do I need to work on ribo- depleted/ ribo zero library generated data or not?

Thanks

Answer 1

[Asaf]

Yes.

Otherwise ~90% of the reads will be of rRNAs. Make sure you don't throw away short RNAs which will probably enriched with IGR encoded RNAs.