I have rna-seq data that comes from a pool of evolved and reference bacterial strains. I would like to know if there has been any mutations in the genes in mutated strains, but can't afford genomics to find them. Is there any way/package to find mutations using my rna-seq data? They're all 2 × 150 bp.
RNAseq data is not tested for variant calling vigorously. You can try the tutorial here: https://ssvbio.github.io/rna-seq-and-gatk-best-practices. In tutorial, tophat is used as tutorial is old. You can use hisat2 instead of tophat and probably you can skip step 9.