Running Salmon on prokaryotic RNA-seq data from Mycobacterium tuberculosis results in only one transcript being detected. What could be the cause of this, and how can I resolve it?
Hi @Chipo_Manda,
We need a lot more information to be able to help here 
What pipeline were you running? What was the command, the log output? What were the Nextflow configs, what was your input data? What did the pipeline reports look like?
The more information you can attach, the more likely it is that someone will be able to help 
Phil