I was wondering if there is a way to obtain/predict 5′-UTRs for bacteria given i have RNA seq data, a complete genome sequence of the bacteria as well. There seems to be no databases dedicated to this for prokaryotes. Any tools if available would also be welcome
thanks
1 answer
See https://www.biostars.org/p/209912/#209912 for a previous discussion regarding this question.
tl;dr while you can't as precisely identify transcription start sites with traditional RNA-seq as compared to say TSS-seq or dRNA-seq there are tools that will predict TSS from RNA-seq. Keep in mind you will be largely limited to the distal most TSS for a transcript when predicting TSS from RNA-seq data.
For bacterial data specifically I recommend first reviewing https://pubmed.ncbi.nlm.nih.gov/25947005/
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