I have been trying to align E. coli mirnome data. For other species, I see that many people have suggested to use the data available on mirbase to use as reference, but it doesn't have a reference for E. coli. When I used the gft available on NCBI, no counts were given by featurecounts. I looked over the gtf file and could not find any miRNA annotation, so I thought this might be the issue. I have considered perhaps using the supplementary data given from this 2013 article to align my data. Is this the correct course of action?
RNACentral has plenty of E coli RNA's: https://rnacentral.org/search?q=Escherichia%20coli
Limit the search based on what kind of RNA you are looking for (filters in left column).
thanks! however, shouldn't it also have a gtf/gff file with the annotations?