Pretty much what the title says.
- What happens if I don't provide a BAI file when it's required? For example, when running RSeQC. The tool still runs, but does it mean it's just slower or my results are wrong too?
- It looks like rsem-calculate-expression does not require a BAI file. Am I correct? Or it does require it but just not warning me when it's not provided? I'm passing my transcriptome BAM from STAR to it.