sarahjeeeze
commented
6 months ago Hi, yes it should work for prokaryotes. In the default reference based mode we only keep the primary alignments from the alignment step to be used in the rest of the analysis workflow, I will update the documentation to mention this. Let me know if you have any issues.
Ask away!
Hello, I don't see any reason why this workflow would not work for prokaryotes. One question I have is how the workflow handles multimapping reads since we plan on getting full-length operon reads so this will be a multimapping issue since reads would map to multiple genes. Any guidance or thoughts on how to deal with that if I need to tweak some settings? Thanks!