I am doing an RNAseq study with isogenic strains of Bacillus subtilis. The background strain I am using is very closely related to a well-annotated genome (strain 168), but has 3 important genes from strain 3610 inserted into the genome. Among other things, I am interested in transcription changes to these insertions and in their vicinity.
I am trying out both CLCworkbench(mapping)/DESEQ2(dif exp analysis) and Rockhopper to look for differential gene expression. However, I have not yet been able to find a straightforward way to edit the genbank annotated reference sequence for B. subtilis available on NCBI (NC_000964). What tools exist to facilitate editing of these files? Are there any that do not require knowledge of python or perl (but I am familiar with R). This does not appear to be a trivial process.